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tag_pileup_frequency test fixes #2727

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merged 8 commits into from
Dec 5, 2019
Merged

tag_pileup_frequency test fixes #2727

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d050c79
tag_pileup_frequency test fixes
gregvonkuster Dec 2, 2019
3abe7ed
Update requirements and reset test to use name attribute
gregvonkuster Dec 4, 2019
6040fcd
Eliminate heatmap outputs in test since no way to set dynamically gen…
gregvonkuster Dec 4, 2019
ef4e741
Fi symlinking to inputs, use element_identifiers as filename
mvdbeek Dec 5, 2019
3f6cf14
Revert "Eliminate heatmap outputs in test since no way to set dynamic…
mvdbeek Dec 5, 2019
d14da26
Oops
mvdbeek Dec 5, 2019
19918fe
Fix output collection assertions
mvdbeek Dec 5, 2019
2857394
Drop fonts package, seem this tool doesn't do any plotting
mvdbeek Dec 5, 2019
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25 changes: 15 additions & 10 deletions tools/tag_pileup_frequency/tag_pileup_frequency.xml
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Original file line number Diff line number Diff line change
@@ -1,15 +1,20 @@
<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1">
<description></description>
<requirements>
<requirement type="package" version="8.0.112">openjdk</requirement>
<requirement type="package" version="11.0.1">openjdk</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
#import re
#set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier))
#set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier))
mkdir -p output &&
ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' &&
ln -s '${input1}' '${input1_identifier}' &&
ln -s '${input2}' '${input2_identifier}' &&
ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' &&
java -jar '$__tool_directory__/TagPileup.jar'
-b '$input1'
-i '${input1}.bai'
-c '$input2'
-b '${input1_identifier}'
-i '${input1_identifier}.bai'
-c '$input2_identifier'
-s $tag_shift
-n $bin_size
-e $tags_equal
Expand All @@ -33,13 +38,13 @@ java -jar '$__tool_directory__/TagPileup.jar'
<param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
<param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
<param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
<option value="0" selected="True">Read1</option>
<option value="0" selected="true">Read1</option>
<option value="1">Read2</option>
<option value="2">combined</option>
</param>
<param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
<param name="combine_strands" type="select" label="Combine strands?">
<option value="0" selected="True">No</option>
<option value="0" selected="true">No</option>
<option value="1">Yes</option>
</param>
<param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
Expand All @@ -64,10 +69,10 @@ java -jar '$__tool_directory__/TagPileup.jar'
<param name="combine_strands" value="0" />
<param name="composite_smoothing_window" value="0" />
<param name="output_heatmap" value="true" />
<output name="output1" file="output1.tabular" ftype="tabular"/>
<output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/>
<output_collection name="heatmaps" type="list">
<element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
<element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
<element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
<element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
</output_collection>
</test>
</tests>
Expand Down
4 changes: 2 additions & 2 deletions tools/tag_pileup_frequency/test-data/output1.tabular
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
-28.0 -27.0 -26.0 -25.0 -24.0 -23.0 -22.0 -21.0 -20.0 -19.0 -18.0 -17.0 -16.0 -15.0 -14.0 -13.0 -12.0 -11.0 -10.0 -9.0 -8.0 -7.0 -6.0 -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0
dataset_2_dataset_1_read1_sense.tabular 0.3170731707317073 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
dataset_2_dataset_1_read1_anti.tabular 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0
tabular 0.3170731707317073 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
.tabular 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0