Mercurial > repos > iuc > irissv

annotate irissv.xml @ 2:6f3e5e591f0b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
author iuc
date Wed, 06 Jul 2022 07:06:50 +0000
parents 9cba5b855260
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
2 <description>Refine insertion sequences</description>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
3 <macros>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
5 </macros>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
6
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
9
2
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
11 @REF_FASTA@
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
12
2
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
13 ln -s '$in_bam' reads.bam &&
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
14 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
15
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
16 iris
1
9cba5b855260 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
iuc
parents: 0
diff changeset
17 genome_in=reference
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
18 vcf_in='${in_vcf}'
2
6f3e5e591f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
iuc
parents: 1
diff changeset
19 reads_in='reads.bam'
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
20 vcf_out='${out_vcf}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
21 threads=\${GALAXY_SLOTS:-4}
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
22 padding_before='${padding_before}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
23 padding_after='${padding_after}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
24 genome_buffer='${genome_buffer}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
25 min_ins_length='${min_ins_length}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
26 max_ins_dist='${max_ins_dist}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
27 max_out_length='${max_out_length}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
28 max_len_change='${max_len_change}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
29 '${aligner}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
30 '${rerunracon}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
31 '${also_deletions}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
32 '${keep_long_variants}'
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
33 ]]></command>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
34 <inputs>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
35 <!--
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
36 Required arguments
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
37 -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
38 <expand macro="reference"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
39 <param name="in_vcf" type="data" format="vcf" label="The VCF file with variant calls/supporting reads"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
40 <param name="in_bam" type="data" format="bam" label="The BAM file containing the reads"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
41 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
42 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
43 <!--
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
44 Optional arguments
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
45 -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
46 <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
47 <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
48 <param argument="genome_buffer" type="integer" value="100000" min="1" label="The genome region on each side of the SV to align assembled reads to" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
49 <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
50 <param argument="max_ins_dist" type="integer" value="100" min="0" label="The max distance a refined insertion call can be from its old position" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
51 <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
52 <param argument="max_len_change" type="float" value="0.25" min="0.0" label="The max proportion by which a variant's length can change" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
53
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
54 <param name="aligner" type="select">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
55 <option value="" selected="true">Use minimap2 for mapping</option>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
56 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
57 <option value="--hifi">Use minimap2 in hifi mode</option>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
58 </param>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
59 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" />
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
60 <!--
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
61 Flags
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
62 -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
63 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
64 <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
65 </inputs>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
66 <outputs>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
67 <!-- standard -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
68 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
69 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
70 <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
71 <filter>output_log</filter>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
72 </data> -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
73 </outputs>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
74 <tests>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
75 <!-- #1 default -->
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
76 <test expect_num_outputs="1">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
77 <conditional name="reference_source">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
78 <param name="reference_source_selector" value="history"/>
1
9cba5b855260 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
iuc
parents: 0
diff changeset
79 <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/>
0
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
80 </conditional>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
81 <param name="in_vcf" value="sniffles.vcf"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
82 <param name="in_bam" value="iris.bam"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
83 <output name="out_vcf" file="test_out.vcf"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
84 </test>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
85 <test expect_num_outputs="1">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
86 <conditional name="reference_source">
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
87 <param name="reference_source_selector" value="cached"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
88 <param name="ref_file" value="iris"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
89 </conditional>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
90 <param name="in_vcf" value="sniffles.vcf"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
91 <param name="in_bam" value="iris.bam"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
92 <output name="out_vcf" file="test_out.vcf"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
93 </test>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
94 </tests>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
95 <help><![CDATA[
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
96 .. class:: infomark
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
97
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
98 **What it does**
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
99
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
100 @WID@
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
101
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
102
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
103 **Input**
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
104
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
105 - FASTA file containing the reference genome
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
106
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
107 - VCF file with variant calls & supporting reads determined by Sniffles
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
108
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
109 - BAM file containing the reads
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
110
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
111 **Output**
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
112
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
113 - VCF file with refined insertion sequences
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
114
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
115 **References**
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
116
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
117 @REFERENCES@
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
118 ]]></help>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
119 <expand macro="citations"/>
1aa0f69923a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
120 </tool>