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comparison stats.xml @ 0:8d02c649a347 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:40:00 +0000
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children 4c6af50296d0
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-1:000000000000 0:8d02c649a347
1 <tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
2 <description>Calculates pairs statistics for input pairs and pairsam files.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 pairtools stats
9 $merge
10 $with_chromsizes
11 $yaml
12 -o '$pairs_output'
13 --nproc-in \${GALAXY_SLOTS:-4}
14 --nproc-out \${GALAXY_SLOTS:-4}
15 #if $input_file:
16 ${str($input_file).replace(',', ' ')}
17 #end if
18 ]]></command>
19 <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>
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>
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>
23 <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
24 </inputs>
25 <outputs>
26 <data name="pairs_output" format="tabular" label="${tool.name} on ${on_string}"/>
27 </outputs>
28 <tests>
29 <!--Test 01 with pair file as input and default parameters-->
30 <test expect_num_outputs="1">
31 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
32 <param name="merge" value="false"/>
33 <param name="with_chromsizes" value="false"/>
34 <param name="yaml" value="false"/>
35 <output name="pairs_output" ftype="tabular" file="pairs_output.stats"/>
36 </test>
37 <!--Test 02 with multipe input pair files as input and default parameters-->
38 <test expect_num_outputs="1">
39 <param name="input_file" value="pairs_output.stats,pairs_output2.stats"/>
40 <param name="merge" value="true"/>
41 <param name="with_chromsizes" value="false"/>
42 <param name="yaml" value="false"/>
43 <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
44 </test>
45 <!--Test 03 with pair files as input with additional chromsizes in output-->
46 <test expect_num_outputs="1">
47 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
48 <param name="merge" value="false"/>
49 <param name="with_chromsizes" value="true"/>
50 <param name="yaml" value="false"/>
51 <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
52 </test>
53 <!--Test 04 with pair files as input and yaml output format-->
54 <test expect_num_outputs="1">
55 <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
56 <param name="merge" value="false"/>
57 <param name="with_chromsizes" value="false"/>
58 <param name="yaml" value="true"/>
59 <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
60 </test>
61 </tests>
62 <help><![CDATA[
63
64 Calculate pairs statistics.
65
66 By default, uses 4dn pairs or 4dn pairsam file to calculate statistics.
67
68 ]]></help>
69 <expand macro="citations"/>
70 </tool>