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comparison sort.xml @ 0:e90acf67d632 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:40:15 +0000
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children 19f062c42798
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-1:000000000000 0:e90acf67d632
1 <tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
2 <description>Sort a 4dn pairs/pairsam file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 pairtools sort
9 '$pairs_path'
10 -o '$output_sorted_pairs'
11 --nproc-in \${GALAXY_SLOTS:-4}
12 --nproc-out \${GALAXY_SLOTS:-4}
13 ]]></command>
14 <inputs>
15 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/>
16 </inputs>
17 <outputs>
18 <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
19 </data>
20 </outputs>
21 <tests>
22 <!--Test default parameters with pairs file-->
23 <test expect_num_outputs="1">
24 <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/>
25 <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/>
26 </test>
27 <!--Test default parameters with pairsam file-->
28 <test expect_num_outputs="1">
29 <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/>
30 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/>
31 </test>
32
33 </tests>
34 <help><![CDATA[
35 **Pairtools sort**
36
37 Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type.
38
39 ]]></help>
40 <expand macro="citations"/>
41 <expand macro="creator"/>
42 </tool>