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comparison parse.xml @ 0:3b5ee2bf3679 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
author iuc
date Sun, 22 Dec 2024 15:39:08 +0000
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children d8e28fa369e1
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-1:000000000000 0:3b5ee2bf3679
1 <tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" 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 #if str($assembly_name).strip():
12 --assembly '$assembly_name'
13 #end if
14 -o '$output_parsed_pairs'
15 --min-mapq '$min_mapq'
16 --max-molecule-size '$max_molecule_size'
17 $drop_readid
18 $drop_seq
19 $output_stats
20 $drop_sam
21 #if $output_stats:
22 '$parsed_pairs_stats'
23 #end if
24 --walks-policy '$walks_policy'
25 --max-inter-align-gap '$max_inter_algn_gap'
26 --nproc-in \${GALAXY_SLOTS:-4}
27 --nproc-out \${GALAXY_SLOTS:-4}
28 ]]></command>
29 <inputs>
30 <param name="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules."/>
31 <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."/>
32 <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
33 <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
34 <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>
35 <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
36 <param argument="--drop-seq" type="boolean" truevalue="--drop-seq" falsevalue="" checked="False" label="remove sequences and PHREDs from the sam fields"></param>
37 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>
38 <param argument="--drop-sam" type="boolean" truevalue="--drop-sam" falsevalue="" checked="False" label="Do not add sams to the output"></param>
39 <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
40 <expand macro="walks_policy_options"/>
41 </param>
42 <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."/>
43 </inputs>
44 <outputs>
45 <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
46 <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
47 <filter>output_stats</filter>
48 </data>
49 </outputs>
50 <tests>
51 <!--Test 01 with SAM file as input and default parameters-->
52 <test expect_num_outputs="1">
53 <param name="sam_path" value="test.sam"/>
54 <param name="chroms_path" value="test.genome"/>
55 <param name="min_mapq" value="1"/>
56 <param name="walks_policy" value="mask"/>
57 <param name="max_inter_algn_gap" value="20"/>
58 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
59 </test>
60 <!--Test 02 with BAM file as input and default parameters-->
61 <test expect_num_outputs="1">
62 <param name="sam_path" value="test.bam"/>
63 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
64 <param name="min_mapq" value="1"/>
65 <param name="walks_policy" value="mask"/>
66 <param name="max_inter_algn_gap" value="20"/>
67 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
68 </test>
69 <!--Test 03 with BAM file as input and minimal mapq of 40-->
70 <test expect_num_outputs="1">
71 <param name="sam_path" value="test.bam"/>
72 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
73 <param name="min_mapq" value="40"/>
74 <param name="walks_policy" value="mask"/>
75 <param name="max_inter_algn_gap" value="20"/>
76 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
77 </test>
78 <!--Test 04 with BAM file as input and walk policy of 5unique-->
79 <test expect_num_outputs="1">
80 <param name="sam_path" value="test.bam"/>
81 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
82 <param name="min_mapq" value="40"/>
83 <param name="walks_policy" value="5unique"/>
84 <param name="max_inter_algn_gap" value="20"/>
85 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
86 </test>
87 <!--Test 05 with BAM file as input and read id dropped-->
88 <test expect_num_outputs="1">
89 <param name="sam_path" value="test.bam"/>
90 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
91 <param name="min_mapq" value="40"/>
92 <param name="walks_policy" value="5unique"/>
93 <param name="max_inter_algn_gap" value="20"/>
94 <param name="drop_readid" value="true"></param>
95 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
96 </test>
97 <!--Test 06 with SAM file as input and drop_seq enabled-->
98 <test expect_num_outputs="1">
99 <param name="sam_path" value="test.sam"/>
100 <param name="chroms_path" value="test.genome"/>
101 <param name="min_mapq" value="40"/>
102 <param name="walks_policy" value="5unique"/>
103 <param name="max_inter_algn_gap" value="20"/>
104 <param name="drop_seq" value="true"></param>
105 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
106 </test>
107 <!--Test 07 with SAM file as input and output_stats enabled-->
108 <test expect_num_outputs="2">
109 <param name="sam_path" value="test.sam"/>
110 <param name="chroms_path" value="test.genome"/>
111 <param name="min_mapq" value="40"/>
112 <param name="walks_policy" value="5unique"/>
113 <param name="max_inter_algn_gap" value="20"/>
114 <param name="output_stats" value="true"></param>
115 <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
116 </test>
117 <!--Test 08 with SAM file as input and default parameters and assembly name -->
118 <test expect_num_outputs="1">
119 <param name="sam_path" value="test.sam"/>
120 <param name="chroms_path" value="test.genome"/>
121 <param name="assembly_name" value="test_assembly"/>
122 <param name="min_mapq" value="1"/>
123 <param name="walks_policy" value="mask"/>
124 <param name="max_inter_algn_gap" value="20"/>
125 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
126 </test>
127
128 </tests>
129 <help><![CDATA[
130 **Pairtools parse**
131
132 Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
133
134 sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules.
135
136 ]]></help>
137 <expand macro="citations"/>
138 <expand macro="creator"/>
139 </tool>