Mercurial > repos > iuc > pairtools_sort

comparison sort.xml @ 2:19f062c42798 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 05:57:12 +0000
parents e90acf67d632
children
comparison
equal deleted inserted replaced
1:be9d6377a908 2:19f062c42798
1 <tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> 1 <tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
2 <description>Sort a 4dn pairs/pairsam file</description> 2 <description>Sort a 4dn pairs/pairsam file</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 $pairs_path.is_of_type('4dn_pairs.gz') or $pairs_path.is_of_type('4dn_pairsam.gz'):
9 #set $input_link = "input.gz"
10 #set $output_sorted_pairs_link = "sorted_output.gz"
11 #else
12 #set $input_link = "input"
13 #set $output_sorted_pairs_link = "sorted_output"
14 #end if
15 ln -s '$pairs_path' '$input_link' &&
16 ln -s '$output_sorted_pairs' '$output_sorted_pairs_link' &&
8 pairtools sort 17 pairtools sort
9 '$pairs_path' 18 '$input_link'
10 -o '$output_sorted_pairs' 19 -o '$output_sorted_pairs_link'
11 --nproc-in \${GALAXY_SLOTS:-4} 20 --nproc-in \${GALAXY_SLOTS:-4}
12 --nproc-out \${GALAXY_SLOTS:-4} 21 --nproc-out \${GALAXY_SLOTS:-4}
13 ]]></command> 22 ]]></command>
14 <inputs> 23 <inputs>
15 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/> 24 <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" label="Input file" help="Input a 4dn pairs or pairsam file"/>
16 </inputs> 25 </inputs>
17 <outputs> 26 <outputs>
18 <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}"> 27 <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
19 </data> 28 </data>
20 </outputs> 29 </outputs>
21 <tests> 30 <tests>
22 <!--Test default parameters with pairs file--> 31 <!--Test default parameters with pairs file, this us actually a pairsam file-->
23 <test expect_num_outputs="1"> 32 <test expect_num_outputs="1">
24 <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/> 33 <param name="pairs_path" ftype="4dn_pairsam" value="output_parsed_pairs_bam.pairs"/>
25 <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/> 34 <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" ftype="4dn_pairsam" lines_diff="10"/>
26 </test> 35 </test>
27 <!--Test default parameters with pairsam file--> 36 <!--Test default parameters with pairsam file-->
28 <test expect_num_outputs="1"> 37 <test expect_num_outputs="1">
29 <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/> 38 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
30 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/> 39 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
31 </test> 40 </test>
32 41 <!--Test default parameters with pairsam file compressed output-->
42 <test expect_num_outputs="1">
43 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam"/>
44 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" decompress="true" lines_diff="10"/>
45 </test>
46 <!--Test default parameters with pairsam file compressed input-->
47 <test expect_num_outputs="1">
48 <param name="pairs_path" ftype="4dn_pairsam" value="output_dedup_pairs_markdups.pairsam.gz"/>
49 <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" ftype="4dn_pairsam" lines_diff="10"/>
50 </test>
33 </tests> 51 </tests>
34 <help><![CDATA[ 52 <help><![CDATA[
35 **Pairtools sort** 53 **Pairtools sort**
36 54
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. 55 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.