Mercurial > repos > iuc > pairtools_split

comparison split.xml @ 2:885b3664540a 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 abd18c860877b2100e02019b4b597d6d2569994e
author iuc
date Thu, 18 Sep 2025 05:56:14 +0000
parents 8ca8c65fc33f
children
comparison
equal deleted inserted replaced
1:6374475dd766 2:885b3664540a
1 <tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> 1 <tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
2 <description>Split a pairsam file into pairs and SAM/BAM</description> 2 <description>Split a pairsam file into pairs and SAM/BAM</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 $pairsam_path.is_of_type('4dn_pairsam.gz'):
9 #set $input_link = "input.gz"
10 #set $output_pairs_link = "output_pairs.gz"
11 #else
12 #set $input_link = "input"
13 #set $output_pairs_link = "output_pairs"
14 #end if
15 ln -s '$pairsam_path' '$input_link' &&
16 ln -s '$output_pairs' '$output_pairs_link' &&
8 pairtools split 17 pairtools split
9 '$pairsam_path' 18 '$input_link'
10 --output-pairs '$output_pairs' 19 --output-pairs '$output_pairs_link'
11 --output-sam ./output.bam 20 --output-sam ./output.bam
12 --nproc-in \${GALAXY_SLOTS:-4} 21 --nproc-in \${GALAXY_SLOTS:-4}
13 --nproc-out \${GALAXY_SLOTS:-4} 22 --nproc-out \${GALAXY_SLOTS:-4}
14 ]]></command> 23 ]]></command>
15 <inputs> 24 <inputs>
16 <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/> 25 <param name="pairsam_path" type="data" format="4dn_pairsam,4dn_pairsam.gz" label="Input 4dn pairsam file"/>
17 </inputs> 26 </inputs>
18 <outputs> 27 <outputs>
19 <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" /> 28 <data name="output_pairs" label="${tool.name} on ${on_string}: Output Pairs" auto_format="true" />
20 <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" /> 29 <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" />
21 </outputs> 30 </outputs>
22 <tests> 31 <tests>
23 <!--Test default parameters--> 32 <!--Test default parameters-->
24 <test expect_num_outputs="2"> 33 <test expect_num_outputs="2">
25 <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/> 34 <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"/> 35 <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs" lines_diff="10"/>
36 <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
37 </test>
38 <!--Test default parameters and compressed input and output-->
39 <test expect_num_outputs="2">
40 <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam.gz"/>
41 <output name="output_pairs" file="output_pairs_split.pairs" ftype="4dn_pairs.gz" decompress="true" lines_diff="10"/>
27 <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/> 42 <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
28 </test> 43 </test>
29 </tests> 44 </tests>
30 <help><![CDATA[ 45 <help><![CDATA[
31 **Pairtools split** 46 **Pairtools split**