| Previous changeset 2:6432735cdb22 (2017-06-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f" |
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modified:
tag_pileup_frequency.xml test-data/output1.tabular |
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| diff -r 6432735cdb22 -r 580e8bcb6413 tag_pileup_frequency.xml --- a/tag_pileup_frequency.xml Fri Jun 16 14:13:32 2017 -0400 +++ b/tag_pileup_frequency.xml Fri Dec 06 15:32:39 2019 -0500 |
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| @@ -1,15 +1,20 @@ -<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1"> +<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2"> <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 @@ -33,13 +38,13 @@ <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)" /> @@ -64,10 +69,10 @@ <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> |
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| diff -r 6432735cdb22 -r 580e8bcb6413 test-data/output1.tabular --- a/test-data/output1.tabular Fri Jun 16 14:13:32 2017 -0400 +++ b/test-data/output1.tabular Fri Dec 06 15:32:39 2019 -0500 |
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| @@ -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 |