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comparison stats.xml @ 2:4c6af50296d0 draft

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planemo upload for repository https://github.com/open2c/pairtools commit abd18c860877b2100e02019b4b597d6d2569994e
author iuc
date Thu, 18 Sep 2025 05:57:30 +0000
parents 8d02c649a347
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1:2212f1654177 2:4c6af50296d0
1 <tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> 1 <tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
2 <description>Calculates pairs statistics for input pairs and pairsam files.</description> 2 <description>Calculates pairs statistics for input pairs and pairsam files.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $merge:
9 #set $input_file_links = str($input_file).replace(',', ' ')
10 #else
11 #set $input_file_links = ""
12 #for $i, $f in enumerate($input_file):
13 #if $f.is_of_type('4dn_pairs.gz') or $f.is_of_type('4dn_pairsam.gz'):
14 ln -s '$f' 'input_file_${i}.gz' &&
15 #set $input_file_links += ' input_file_%d.gz ' % $i
16 #else:
17 ln -s '$f' 'input_file_${i}' &&
18 #set $input_file_links += ' input_file_%d ' % $i
19 #end if
20 #end for
21 #end if
22
8 pairtools stats 23 pairtools stats
9 $merge 24 $merge
10 $with_chromsizes 25 $with_chromsizes
11 $yaml 26 $yaml
12 -o '$pairs_output' 27 -o '$pairs_output'
13 --nproc-in \${GALAXY_SLOTS:-4} 28 --nproc-in \${GALAXY_SLOTS:-4}
14 --nproc-out \${GALAXY_SLOTS:-4} 29 --nproc-out \${GALAXY_SLOTS:-4}
15 #if $input_file: 30 $input_file_links
16 ${str($input_file).replace(',', ' ')}
17 #end if
18 ]]></command> 31 ]]></command>
19 <inputs> 32 <inputs>
20 <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param> 33 <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
21 <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param> 34 <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param>
22 <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param> 35 <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param>
23 <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param> 36 <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
24 </inputs> 37 </inputs>
25 <outputs> 38 <outputs>
42 <param name="yaml" value="false"/> 55 <param name="yaml" value="false"/>
43 <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/> 56 <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
44 </test> 57 </test>
45 <!--Test 03 with pair files as input with additional chromsizes in output--> 58 <!--Test 03 with pair files as input with additional chromsizes in output-->
46 <test expect_num_outputs="1"> 59 <test expect_num_outputs="1">
47 <param name="input_file" value="output_parsed_pairs_sam.pairs"/> 60 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs"/>
48 <param name="merge" value="false"/> 61 <param name="merge" value="false"/>
49 <param name="with_chromsizes" value="true"/> 62 <param name="with_chromsizes" value="true"/>
50 <param name="yaml" value="false"/> 63 <param name="yaml" value="false"/>
51 <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/> 64 <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
52 </test> 65 </test>
53 <!--Test 04 with pair files as input and yaml output format--> 66 <!--Test 04 with pair files as input and yaml output format-->
54 <test expect_num_outputs="1"> 67 <test expect_num_outputs="1">
55 <param name="input_file" value="output_parsed_pairs_sam.pairs"/> 68 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs"/>
69 <param name="merge" value="false"/>
70 <param name="with_chromsizes" value="false"/>
71 <param name="yaml" value="true"/>
72 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
73 </test>
74 <!--Test 05 with compressed input pair file as input and default parameters-->
75 <test expect_num_outputs="1">
76 <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs.gz"/>
56 <param name="merge" value="false"/> 77 <param name="merge" value="false"/>
57 <param name="with_chromsizes" value="false"/> 78 <param name="with_chromsizes" value="false"/>
58 <param name="yaml" value="true"/> 79 <param name="yaml" value="true"/>
59 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/> 80 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
60 </test> 81 </test>
61 </tests> 82 </tests>
62 <help><![CDATA[ 83 <help><![CDATA[
63 84
64 Calculate pairs statistics. 85 Calculate pairs statistics.
65 86
66 By default, uses 4dn pairs or 4dn pairsam file to calculate statistics. 87 By default, uses 4dn pairs or 4dn pairsam file to calculate statistics. Setting merge to true will
88 merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file.
67 89
68 ]]></help> 90 ]]></help>
69 <expand macro="citations"/> 91 <expand macro="citations"/>
70 </tool> 92 </tool>