Merge branch 'master' into lint_skip

tools/diff/diff.xml

@@ -1,7 +1,7 @@
-<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
     <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.7</token>
+        <token name="@TOOL_VERSION@">3.10</token>
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <requirements>
@@ -13,10 +13,18 @@
         <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
     </stdio>
     <command><![CDATA[
-        diff -u '$input1' '$input2' > '$diff_file';
-        #if $generate_report:
+        diff
+        #if $report_format.report_format_select == 'txt_lines' or $report_format.report_format_select == 'html'
+            ## the -u option is needed to convert the output later to HTML
+            --unified=$report_format.unified
+        #else if $report_format.report_format_select == 'txt_columns'
+            -y
+        #end if
+        ## If the compared input files differ the diff command returns exit-code 1
+        '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
+        #if $report_format.report_format_select == 'html'
             sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-                -e 's/@@outputformat@@/'$output_format'/g'
+                -e 's/@@outputformat@@/'$report_format.output_format'/g'
                 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                 '$__tool_directory__/template.html' > '$html_file'
         #end if
@@ -25,33 +33,50 @@
     <inputs>
         <param name="input1" type="data" format="txt" label="First input file"/>
         <param name="input2" type="data" format="txt" label="Second input file"/>
-        <param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/>
-        <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
-            <option value="side-by-side">Side by side</option>
-            <option value="line-by-line">Line by line</option>
-        </param>
+        <conditional name="report_format">
+            <param name="report_format_select" type="select" label="Choose a report format">
+                <option value="txt_lines">Text file, line-by-line (-u)</option>
+                <option value="txt_columns">Text file, side-by-side (-y)</option>
+                <option value="html">Generates an HTML report to visualize the differences</option>
+            </param>
+            <when value="txt_lines">
+                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
+            </when>
+            <when value="txt_columns"/>
+            <when value="html">
+                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
+                <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
+                    <option value="side-by-side">Side by side</option>
+                    <option value="line-by-line">Line by line</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
         <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
-            <filter>generate_report is True</filter>
+            <filter>report_format['report_format_select'] == 'html'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file1.txt"/>
-            <param name="generate_report" value="false"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
+        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="false"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="txt_lines"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="5"/>
@@ -63,7 +88,9 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -73,8 +100,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
-            <param name="output_format" value="side-by-side"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -85,8 +114,10 @@
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
             <param name="input1" value="file1.txt"/>
             <param name="input2" value="file2.txt"/>
-            <param name="generate_report" value="true"/>
-            <param name="output_format" value="line-by-line"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="line-by-line"/>
+            </conditional>
             <output name="html_file">
                 <assert_contents>
                     <has_text text="!DOCTYPE html"/>
@@ -95,9 +126,12 @@
             </output>
         </test>
         <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
-            <param name="input1" value="file 3.txt"/>
-            <param name="input2" value="file 3.txt"/>
-            <param name="generate_report" value="true"/>
+            <param name="input1" value="file3.txt"/>
+            <param name="input2" value="file3.txt"/>
+            <conditional name="report_format">
+                <param name="report_format_select" value="html"/>
+                <param name="output_format" value="side-by-side"/>
+            </conditional>
             <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="0"/>
@@ -169,4 +203,4 @@ An **optional** *HTML report* with a friendlier visual representation of the dif
             }
         </citation>
     </citations>
-</tool>
+</tool>

tools/diff/test-data/output_test4.txt

@@ -0,0 +1,2 @@
+a								a
+							      >	b

tools/gfastats/gfastats.xml

@@ -111,7 +111,7 @@
             </param>
             <when value="manipulation">
                 <param argument="--swiss-army-knife" type="data"
-                    format="text" label="SAK input file" optional="true"
+                    format="txt" label="SAK input file" optional="true"
                     help="Set of instructions provided as an ordered list"/>
                 <conditional name="output_condition">
                     <param argument="--out-format" type="select" 
@@ -201,7 +201,7 @@
         <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
             <filter>mode_condition['selector'] == 'statistics'</filter>
             <change_format>
-                <when input="tabular" value="false" format="text"/>
+                <when input="tabular" value="false" format="txt"/>
             </change_format>
         </data>
         <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">

tools/gfastats/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.9</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">gfastats</requirement>

tools/music_deconvolution/.shed.yml

@@ -4,7 +4,7 @@ description: "Multi-subject Single Cell deconvolution (MuSiC)"
 homepage_url: https://github.com/xuranw/MuSiC
 long_description: |
     MuSiC is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution
 type: unrestricted
 categories:
 - Transcriptomics

tools/wordcloud/.shed.yml

@@ -0,0 +1,12 @@
+name: wordcloud
+owner: bgruening
+description: A little word cloud generator in Python.
+long_description: |
+  The wordcloud library allows you to create word clouds from text data.
+  It is highly customizable and can generate word clouds in various shapes and colors.
+  The wordcloud library is available as an open-source project on GitHub.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud
+homepage_url: https://github.com/amueller/word_cloud
+type:
+categories:
+  - Visualization

tools/wordcloud/test-data/stopwords.txt

@@ -0,0 +1 @@
+an

tools/wordcloud/test-data/test.txt

@@ -0,0 +1 @@
+Galaxy is an open source, web-based platform for data intensive biomedical research.