Mercurial > repos > iuc > tag_pileup_frequency
comparison tag_pileup_frequency.xml @ 3:580e8bcb6413 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
author | iuc |
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date | Fri, 06 Dec 2019 15:32:39 -0500 |
parents | 6432735cdb22 |
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2:6432735cdb22 | 3:580e8bcb6413 |
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1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1"> | 1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="8.0.112">openjdk</requirement> | 4 <requirement type="package" version="11.0.1">openjdk</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 #import re | |
8 #set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier)) | |
9 #set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier)) | |
7 mkdir -p output && | 10 mkdir -p output && |
8 ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' && | 11 ln -s '${input1}' '${input1_identifier}' && |
12 ln -s '${input2}' '${input2_identifier}' && | |
13 ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' && | |
9 java -jar '$__tool_directory__/TagPileup.jar' | 14 java -jar '$__tool_directory__/TagPileup.jar' |
10 -b '$input1' | 15 -b '${input1_identifier}' |
11 -i '${input1}.bai' | 16 -i '${input1_identifier}.bai' |
12 -c '$input2' | 17 -c '$input2_identifier' |
13 -s $tag_shift | 18 -s $tag_shift |
14 -n $bin_size | 19 -n $bin_size |
15 -e $tags_equal | 20 -e $tags_equal |
16 -r $reads | 21 -r $reads |
17 -p $proper_pe | 22 -p $proper_pe |
31 <param name="input2" type="data" format="bed" label="Bed file" /> | 36 <param name="input2" type="data" format="bed" label="Bed file" /> |
32 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> | 37 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> |
33 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> | 38 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> |
34 <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> | 39 <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> |
35 <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> | 40 <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> |
36 <option value="0" selected="True">Read1</option> | 41 <option value="0" selected="true">Read1</option> |
37 <option value="1">Read2</option> | 42 <option value="1">Read2</option> |
38 <option value="2">combined</option> | 43 <option value="2">combined</option> |
39 </param> | 44 </param> |
40 <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> | 45 <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> |
41 <param name="combine_strands" type="select" label="Combine strands?"> | 46 <param name="combine_strands" type="select" label="Combine strands?"> |
42 <option value="0" selected="True">No</option> | 47 <option value="0" selected="true">No</option> |
43 <option value="1">Yes</option> | 48 <option value="1">Yes</option> |
44 </param> | 49 </param> |
45 <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> | 50 <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> |
46 <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> | 51 <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> |
47 </inputs> | 52 </inputs> |
62 <param name="reads" value="0" /> | 67 <param name="reads" value="0" /> |
63 <param name="proper_pe" value="false" /> | 68 <param name="proper_pe" value="false" /> |
64 <param name="combine_strands" value="0" /> | 69 <param name="combine_strands" value="0" /> |
65 <param name="composite_smoothing_window" value="0" /> | 70 <param name="composite_smoothing_window" value="0" /> |
66 <param name="output_heatmap" value="true" /> | 71 <param name="output_heatmap" value="true" /> |
67 <output name="output1" file="output1.tabular" ftype="tabular"/> | 72 <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/> |
68 <output_collection name="heatmaps" type="list"> | 73 <output_collection name="heatmaps" type="list"> |
69 <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> | 74 <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> |
70 <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> | 75 <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> |
71 </output_collection> | 76 </output_collection> |
72 </test> | 77 </test> |
73 </tests> | 78 </tests> |
74 <help> | 79 <help> |
75 | 80 |