Add data collection for input

ISA-tools · Jun 6, 2018 · 8cfba52 · 8cfba52
1 parent 49deaae
commit 8cfba52
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diff --git a/galaxy/mzml2isa/mzml2isa.xml b/galaxy/mzml2isa/mzml2isa.xml
@@ -5,17 +5,18 @@
         <import>mzml2isa_macros.xml</import>
     </macros>
 
-    <code file="ontology_search.py" />
-
     <requirements>
         <requirement type="package" version="0.4.24">mzml2isa</requirement>
     </requirements>
 
+    <code file="ontology_search.py" />
+
     <stdio>
         <exit_code range="1:" />
     </stdio>
 
-    <command interpreter="python"><![CDATA[
+    <command detect_errors="exit_code">
+    <![CDATA[
     #set $s_submission_date = ""
     #set $s_release_date = ""
     #set $s_description = ""
@@ -123,8 +124,27 @@
         #set $organism_part_iri = $exp_meta.organism_part_iri
     #end if
 
+    #if $input.format == "data_collection"
+        mkdir "temp"
+        &&
+        cd "temp"
+        &&
+        #for $fn in $input.source
+            #if str( $fn ).endswith(".dat")
+                ln -s '$fn' '$fn.name'
+                &&
+            #end if
+        #end for
+        cd ..
+        &&
+    #end if
 
-    wrapper.py -inputzip "$inputzip"
+    python $__tool_directory__/wrapper.py
+    #if $input.format == "zip_file"
+         -inputzip "$input.source"
+    #else if $input.format == "data_collection"
+         -folder "temp"
+    #end if
                -jsontxt "$jsontxt"
                -html_file "$html_file"
                -out_dir .
@@ -171,18 +191,37 @@
                --organism_variant_iri "$organism_variant_iri"
                --organism_part_text "$organism_part_text"
                --organism_part_ref "$organism_part_ref"
-	           --organism_part_iri "$organism_part_iri";
+	       --organism_part_iri "$organism_part_iri";
 
 	       ln -s ./"$name_of_study" study_dir;
 
 	       cd study_dir;
 	       zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip";
-	       ]]>
+    ]]>
     </command>
 
     <inputs>
         <param name="name_of_study" type="text" label="Name study" help="This should not contain any spaces as the name will be used a prefix for ISA-tab file names" />
-        <param format="zip" name="inputzip" type="data" label="mzML zip file"  help="A zipped folder of mzML files"/>
+
+        <conditional name="input">
+            <param name="format" type="select" label="Choose the source for the dataset" >
+                <option value="zip_file" selected="true">Zip file from your History containing a folder of *.mzML files</option>
+                <option value="data_collection">Data collection (*.mzML files)</option>
+            </param>
+            <when value="zip_file">
+                <param name="source" type="data" format="zip" label="Zip file from your History containing *.mzml files">
+                    <validator type="empty_field" />
+                </param>
+            </when>
+            <when value="data_collection">
+                <param name="source" type="data_collection" format="mzml" label="Data collection of *.mzml" >
+                    <validator type="empty_field" />
+                </param>
+            </when>
+        </conditional>
+
+        <!--<param format="zip" name="inputzip" type="data" label="mzML zip file"  help="A zipped folder of mzML files"/>-->
+
         <param optional="true" format="txt" name="jsontxt" type="data" label="Additional user Metadata in json"  help="A user can add additional metadata directory through a json file"/>
         <expand macro="studymacro"/>
         <expand macro="investmacro"/>
@@ -211,13 +250,14 @@ this would require changing the out_dir for wrapper.py back to $html_file.extra_
 	<collection type="list" label="S Files" name="s_files">
 		<discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="study_dir" format="tabular"/>
 	</collection>
-	<data name="i_file" format="tabular" label="I File" from_work_dir="study_dir/i_Investigation.txt" visible="true"/>
+	<data name="i_file" format="tabular" label="I File" from_work_dir="study_dir/i_Investigation.txt"/>
     </outputs>
 
     <tests>
         <test>
             <param name="name_of_study" value="test" />
-            <param name="inputzip" value="metabolomics_study.zip" ftype="zip" />
+            <param name="input|format" value="zip_file" />
+            <param name="input|source" value="metabolomics_study.zip" ftype="zip" />
             <output name="html_file" value="metabolomics_study/test/index.html" />
             <output name="i_file" value="metabolomics_study/test/i_Investigation.txt" />
             <output_collection name="a_files" type="list" count="1">
@@ -235,6 +275,36 @@ this would require changing the out_dir for wrapper.py back to $html_file.extra_
                 </element>
             </output_collection>
         </test>
+        <test>
+            <param name="name_of_study" value="test_collection" />
+            <param name="input|format" value="data_collection" />
+            <param name="input|source" >
+                <collection type="list">
+                    <element name="1_samp" value="1_samp.mzML" />
+                    <element name="2_samp" value="2_samp.mzML" />
+                    <element name="3_samp" value="3_samp.mzML" />
+                    <element name="4_samp" value="4_samp.mzML" />
+                    <element name="5_samp" value="5_samp.mzML" />
+                    <element name="6_samp" value="6_samp.mzML" />
+                </collection>
+            </param >
+            <output name="html_file" value="metabolomics_study/test_collection/index.html" />
+            <output name="i_file" value="metabolomics_study/test_collection/i_Investigation.txt" />
+            <output_collection name="a_files" type="list" count="1">
+                <element name="a_test_collection_metabolite_profiling_mass_spectrometry">
+                    <assert_contents>
+                        <has_n_columns n="77" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="s_files" type="list" count="1">
+                <element name="s_test_collection">
+                    <assert_contents>
+                        <has_n_columns n="12" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **Overview**

diff --git a/galaxy/mzml2isa/test-data/1_samp.mzML b/galaxy/mzml2isa/test-data/1_samp.mzML
diff --git a/galaxy/mzml2isa/test-data/2_samp.mzML b/galaxy/mzml2isa/test-data/2_samp.mzML
diff --git a/galaxy/mzml2isa/test-data/3_samp.mzML b/galaxy/mzml2isa/test-data/3_samp.mzML
diff --git a/galaxy/mzml2isa/test-data/4_samp.mzML b/galaxy/mzml2isa/test-data/4_samp.mzML
diff --git a/galaxy/mzml2isa/test-data/5_samp.mzML b/galaxy/mzml2isa/test-data/5_samp.mzML
diff --git a/galaxy/mzml2isa/test-data/6_samp.mzML b/galaxy/mzml2isa/test-data/6_samp.mzML
diff --git a/...lomics_study/test_collection/a_test_collection_metabolite_profiling_mass_spectrometry.txt b/...lomics_study/test_collection/a_test_collection_metabolite_profiling_mass_spectrometry.txt
@@ -0,0 +1,7 @@
+"Sample Name"	"Protocol REF"	"Parameter Value[Post Extraction]"	"Parameter Value[Derivatization]"	"Extract Name"	"Protocol REF"	"Parameter Value[Chromatography Instrument]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Column model]"	"Parameter Value[Column type]"	"Labeled Extract Name"	"Label"	"Term Source REF"	"Term Accession Number"	"Protocol REF"	"Parameter Value[Scan polarity]"	"Parameter Value[Scan m/z range]"	"Unit"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Instrument]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Ion source]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Mass analyzer]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Inlet type]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Detector]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Detector mode]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Native spectrum identifier format]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Data file content]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Data file checksum type]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Raw data file format]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Instrument manufacturer]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Instrument serial number]"	"Parameter Value[Instrument software]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Number of scans]"	"Parameter Value[Time range]"	"Unit"	"Term Source REF"	"Term Accession Number"	"MS Assay Name"	"Raw Spectral Data File"	"Protocol REF"	"Normalization Name"	"Derived Spectral Data File"	"Protocol REF"	"Parameter Value[Data Transformation software]"	"Term Source REF"	"Term Accession Number"	"Parameter Value[Data Transformation software version]"	"Data Transformation Name"	"Term Source REF"	"Term Accession Number"	"Metabolite Assignment File"
+"5_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"5_samp"	""	"Data transformation"	""	"5_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""
+"3_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"3_samp"	""	"Data transformation"	""	"3_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""
+"2_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"2_samp"	""	"Data transformation"	""	"2_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""
+"1_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"1_samp"	""	"Data transformation"	""	"1_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""
+"6_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"6_samp"	""	"Data transformation"	""	"6_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""
+"4_samp"	"Extraction"	""	""	""	"Chromatography"	""	""	""	""	""	""	""	""	""	"Mass spectrometry"	"positive scan"	"140-2000"	"m/z"	"MS"	"http://purl.obolibrary.org/obo/MS_1000040"	"LTQ FT"	"MS"	"http://purl.obolibrary.org/obo/MS_1000448"	"electrospray ionization"	"MS"	"http://purl.obolibrary.org/obo/MS_1000073"	"radial ejection linear ion trap"	"MS"	"http://purl.obolibrary.org/obo/MS_1000083"	"electrospray inlet"	"MS"	"http://purl.obolibrary.org/obo/MS_1000057"	"electron multiplier"	"MS"	"http://purl.obolibrary.org/obo/MS_1000253"	""	""	""	"Thermo nativeID format"	"MS"	"http://purl.obolibrary.org/obo/MS_1000768"	"MSn spectrum"	"MS"	"http://purl.obolibrary.org/obo/MS_1000580"	"SHA-1"	"MS"	"http://purl.obolibrary.org/obo/MS_1000569"	"Thermo RAW file"	"MS"	"http://purl.obolibrary.org/obo/MS_1000563"	"Thermo Fisher Scientific instrument model"	"MS"	"http://purl.obolibrary.org/obo/MS_1000483"	"SN06061F"	"Xcalibur"	"MS"	"http://purl.obolibrary.org/obo/MS_1000532"	"48"	"0.0049-0.4872"	"minute"	"UO"	"http://purl.obolibrary.org/obo/UO_0000031"	"4_samp"	""	"Data transformation"	""	"4_samp.mzML"	"Metabolite identification"	"ProteoWizard"	"MS"	"http://purl.obolibrary.org/obo/MS_1000615"	"1.4.0"	"Conversion to mzML"	"MS"	"http://purl.obolibrary.org/obo/MS_1000544"	""