Mercurial > repos > iuc > pairtools_split

comparison split.xml @ 0:8ca8c65fc33f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:39:27 +0000
parents
children 885b3664540a
comparison
equal deleted inserted replaced
-1:000000000000 0:8ca8c65fc33f
1 <tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
2 <description>Split a pairsam file into pairs and SAM/BAM</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 pairtools split
9 '$pairsam_path'
10 --output-pairs '$output_pairs'
11 --output-sam ./output.bam
12 --nproc-in \${GALAXY_SLOTS:-4}
13 --nproc-out \${GALAXY_SLOTS:-4}
14 ]]></command>
15 <inputs>
16 <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/>
17 </inputs>
18 <outputs>
19 <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" />
20 <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" />
21 </outputs>
22 <tests>
23 <!--Test default parameters-->
24 <test expect_num_outputs="2">
25 <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/>
26 <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/>
27 <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 **Pairtools split**
32
33 Restore a SAM/BAM file from SAM1 and SAM2 fields of a `pairsam` file. Create a `pairs` file without SAM1/SAM2 fields.
34
35 ]]></help>
36 <expand macro="citations"/>
37 <expand macro="creator"/>
38 </tool>