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comparison parse.xml @ 1:8fae6be7a507 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 17acbcae8309bec856882bc4aef1899d613f6807
author iuc
date Wed, 03 Apr 2024 16:25:30 +0000
parents 68413c5eb035
children 26ed6ceeeec1
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0:68413c5eb035 1:8fae6be7a507
1 <tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05" license="MIT"> 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> 2 <description>Find ligation pairs in alignments and create pairs.</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"/>
38 <expand macro="walks_policy_options"/> 38 <expand macro="walks_policy_options"/>
39 </param> 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."/> 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> 41 </inputs>
42 <outputs> 42 <outputs>
43 <data name="output_parsed_pairs" format="pairs" label="${tool.name} on ${on_string}: .pairs"/> 43 <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
44 <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats"> 44 <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
45 <filter>output_stats</filter> 45 <filter>output_stats</filter>
46 </data> 46 </data>
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
51 <param name="sam_path" value="test.sam"/> 51 <param name="sam_path" value="test.sam"/>
52 <param name="chroms_path" value="test.genome"/> 52 <param name="chroms_path" value="test.genome"/>
53 <param name="min_mapq" value="1"/> 53 <param name="min_mapq" value="1"/>
54 <param name="walks_policy" value="mask"/> 54 <param name="walks_policy" value="mask"/>
55 <param name="max_inter_algn_gap" value="20"/> 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"/> 56 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
57 </test> 57 </test>
58 <!--Test 02 with BAM file as input and default parameters--> 58 <!--Test 02 with BAM file as input and default parameters-->
59 <test expect_num_outputs="1"> 59 <test expect_num_outputs="1">
60 <param name="sam_path" value="test.bam"/> 60 <param name="sam_path" value="test.bam"/>
61 <param name="chroms_path" value="test.reduced.chrom.sizes"/> 61 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
62 <param name="min_mapq" value="1"/> 62 <param name="min_mapq" value="1"/>
63 <param name="walks_policy" value="mask"/> 63 <param name="walks_policy" value="mask"/>
64 <param name="max_inter_algn_gap" value="20"/> 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"/> 65 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
66 </test> 66 </test>
67 <!--Test 03 with BAM file as input and minimal mapq of 40--> 67 <!--Test 03 with BAM file as input and minimal mapq of 40-->
68 <test expect_num_outputs="1"> 68 <test expect_num_outputs="1">
69 <param name="sam_path" value="test.bam"/> 69 <param name="sam_path" value="test.bam"/>
70 <param name="chroms_path" value="test.reduced.chrom.sizes"/> 70 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
71 <param name="min_mapq" value="40"/> 71 <param name="min_mapq" value="40"/>
72 <param name="walks_policy" value="mask"/> 72 <param name="walks_policy" value="mask"/>
73 <param name="max_inter_algn_gap" value="20"/> 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"/> 74 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
75 </test> 75 </test>
76 <!--Test 04 with BAM file as input and walk policy of 5unique--> 76 <!--Test 04 with BAM file as input and walk policy of 5unique-->
77 <test expect_num_outputs="1"> 77 <test expect_num_outputs="1">
78 <param name="sam_path" value="test.bam"/> 78 <param name="sam_path" value="test.bam"/>
79 <param name="chroms_path" value="test.reduced.chrom.sizes"/> 79 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
80 <param name="min_mapq" value="40"/> 80 <param name="min_mapq" value="40"/>
81 <param name="walks_policy" value="5unique"/> 81 <param name="walks_policy" value="5unique"/>
82 <param name="max_inter_algn_gap" value="20"/> 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"/> 83 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
84 </test> 84 </test>
85 <!--Test 05 with BAM file as input and read id dropped--> 85 <!--Test 05 with BAM file as input and read id dropped-->
86 <test expect_num_outputs="1"> 86 <test expect_num_outputs="1">
87 <param name="sam_path" value="test.bam"/> 87 <param name="sam_path" value="test.bam"/>
88 <param name="chroms_path" value="test.reduced.chrom.sizes"/> 88 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
89 <param name="min_mapq" value="40"/> 89 <param name="min_mapq" value="40"/>
90 <param name="walks_policy" value="5unique"/> 90 <param name="walks_policy" value="5unique"/>
91 <param name="max_inter_algn_gap" value="20"/> 91 <param name="max_inter_algn_gap" value="20"/>
92 <param name="drop_readid" value="true"></param> 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"/> 93 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
94 </test> 94 </test>
95 <!--Test 06 with SAM file as input and drop_seq enabled--> 95 <!--Test 06 with SAM file as input and drop_seq enabled-->
96 <test expect_num_outputs="1"> 96 <test expect_num_outputs="1">
97 <param name="sam_path" value="test.sam"/> 97 <param name="sam_path" value="test.sam"/>
98 <param name="chroms_path" value="test.genome"/> 98 <param name="chroms_path" value="test.genome"/>
99 <param name="min_mapq" value="40"/> 99 <param name="min_mapq" value="40"/>
100 <param name="walks_policy" value="5unique"/> 100 <param name="walks_policy" value="5unique"/>
101 <param name="max_inter_algn_gap" value="20"/> 101 <param name="max_inter_algn_gap" value="20"/>
102 <param name="drop_seq" value="true"></param> 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"/> 103 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
104 </test> 104 </test>
105 <!--Test 07 with SAM file as input and output_stats enabled--> 105 <!--Test 07 with SAM file as input and output_stats enabled-->
106 <test expect_num_outputs="2"> 106 <test expect_num_outputs="2">
107 <param name="sam_path" value="test.sam"/> 107 <param name="sam_path" value="test.sam"/>
108 <param name="chroms_path" value="test.genome"/> 108 <param name="chroms_path" value="test.genome"/>