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comparison parse.xml @ 0:68413c5eb035 draft

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planemo upload for repository https://github.com/open2c/pairtools commit ccfba0aea1bde83cd14ab0ffc312d96cf13e777f
author iuc
date Tue, 26 Mar 2024 12:49:21 +0000
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1 <tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05" license="MIT">
2 <description>Find ligation pairs in alignments and create pairs.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 pairtools parse
9 '$sam_path'
10 -c '$chroms_path'
11 $assembly
12 -o '$output_parsed_pairs'
13 --min-mapq '$min_mapq'
14 --max-molecule-size '$max_molecule_size'
15 $drop_readid
16 $drop_seq
17 $output_stats
18 $drop_sam
19 #if $output_stats:
20 '$parsed_pairs_stats'
21 #end if
22 --walks-policy '$walks_policy'
23 --max-inter-align-gap '$max_inter_algn_gap'
24 --nproc-in \${GALAXY_SLOTS:-4}
25 --nproc-out \${GALAXY_SLOTS:-4}
26 ]]></command>
27 <inputs>
28 <param name="sam_path" type="data" format="sam,bam" label="Input SAM/BAM file" help="Input SAM or BAM file with paired-end sequence alignments of Hi-C molecules."/>
29 <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
30 <param name="assembly" type="text" value="" label="Input a name of a genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
31 <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
32 <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
33 <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
34 <param argument="--drop-seq" type="boolean" truevalue="--drop-seq" falsevalue="" checked="False" label="remove sequences and PHREDs from the sam fields"></param>
35 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Do not add sams to the output"></param>
36 <param argument="--drop-sam" type="boolean" truevalue="--drop-sam" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>
37 <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
38 <expand macro="walks_policy_options"/>
39 </param>
40 <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
41 </inputs>
42 <outputs>
43 <data name="output_parsed_pairs" format="pairs" label="${tool.name} on ${on_string}: .pairs"/>
44 <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
45 <filter>output_stats</filter>
46 </data>
47 </outputs>
48 <tests>
49 <!--Test 01 with SAM file as input and default parameters-->
50 <test expect_num_outputs="1">
51 <param name="sam_path" value="test.sam"/>
52 <param name="chroms_path" value="test.genome"/>
53 <param name="min_mapq" value="1"/>
54 <param name="walks_policy" value="mask"/>
55 <param name="max_inter_algn_gap" value="20"/>
56 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
57 </test>
58 <!--Test 02 with BAM file as input and default parameters-->
59 <test expect_num_outputs="1">
60 <param name="sam_path" value="test.bam"/>
61 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
62 <param name="min_mapq" value="1"/>
63 <param name="walks_policy" value="mask"/>
64 <param name="max_inter_algn_gap" value="20"/>
65 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
66 </test>
67 <!--Test 03 with BAM file as input and minimal mapq of 40-->
68 <test expect_num_outputs="1">
69 <param name="sam_path" value="test.bam"/>
70 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
71 <param name="min_mapq" value="40"/>
72 <param name="walks_policy" value="mask"/>
73 <param name="max_inter_algn_gap" value="20"/>
74 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
75 </test>
76 <!--Test 04 with BAM file as input and walk policy of 5unique-->
77 <test expect_num_outputs="1">
78 <param name="sam_path" value="test.bam"/>
79 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
80 <param name="min_mapq" value="40"/>
81 <param name="walks_policy" value="5unique"/>
82 <param name="max_inter_algn_gap" value="20"/>
83 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
84 </test>
85 <!--Test 05 with BAM file as input and read id dropped-->
86 <test expect_num_outputs="1">
87 <param name="sam_path" value="test.bam"/>
88 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
89 <param name="min_mapq" value="40"/>
90 <param name="walks_policy" value="5unique"/>
91 <param name="max_inter_algn_gap" value="20"/>
92 <param name="drop_readid" value="true"></param>
93 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
94 </test>
95 <!--Test 06 with SAM file as input and drop_seq enabled-->
96 <test expect_num_outputs="1">
97 <param name="sam_path" value="test.sam"/>
98 <param name="chroms_path" value="test.genome"/>
99 <param name="min_mapq" value="40"/>
100 <param name="walks_policy" value="5unique"/>
101 <param name="max_inter_algn_gap" value="20"/>
102 <param name="drop_seq" value="true"></param>
103 <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
104 </test>
105 <!--Test 07 with SAM file as input and output_stats enabled-->
106 <test expect_num_outputs="2">
107 <param name="sam_path" value="test.sam"/>
108 <param name="chroms_path" value="test.genome"/>
109 <param name="min_mapq" value="40"/>
110 <param name="walks_policy" value="5unique"/>
111 <param name="max_inter_algn_gap" value="20"/>
112 <param name="output_stats" value="true"></param>
113 <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
114 </test>
115
116 </tests>
117 <help><![CDATA[
118 **Pairtools parse**
119
120 Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
121
122 sam_path : an input .sam/.bam file with paired-end sequence alignments of Hi-C molecules.
123
124 ]]></help>
125 <expand macro="citations"/>
126 <expand macro="creator"/>
127 </tool>