Mercurial > repos > jjohnson > shear

annotate shear_sv.xml @ 9:03071ff2e5c9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add cap3 requirement for crest
author Jim Johnson <jj@umn.edu>
date Tue, 22 Oct 2013 09:55:49 -0500
parents 8180f6b0249b
children 2620f7984418
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
1 <?xml version="1.0"?>
7
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 6
diff changeset
2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.3">
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
3 <description>find SVs and estimate the heterogeneity levels from a BAM</description>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
4 <requirements>
7
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 6
diff changeset
5 <requirement type="package" version="0.2.4">shear</requirement>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
6 <requirement type="package" version="0.1.18">samtools</requirement>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
7 <requirement type="package" version="0.6.2">bwa</requirement>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
8 <requirement type="package" version="1.0.1">crest</requirement>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
9 <requirement type="package" version="latest">kent</requirement>
9
03071ff2e5c9 Add cap3 requirement for crest
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
10 <requirement type="package" version="3">cap3</requirement>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
11 </requirements>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
12 <!--
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
13 <version_command></version_command>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
14 -->
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
15 <command interpreter="python">
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
16 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command sv
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
17 -p $prefix ## used in gerenating ouput file names
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
18 -b $bamfile
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
19 #if $genomeSource.refGenomeSource == 'indexed':
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
20 -f $genomeSource.ref_fastas.fields.path
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
21 -i $genomeSource.bwa_indices.fields.path
3
630532975fa9 Fix more typos
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
22 -t $genomeSource.twobit_indices.fields.path
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
23 #elif $genomeSource.refGenomeSource == 'svidx':
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
24 -f $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
25 -i $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
26 -t $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.2bit
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
27 #else:
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
28 -f $genomeSource.ref_fasta
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
29 #if $genomeSource.save_svidx:
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
30 -D $sv_idx.extra_files_path
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
31 #end if
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
32 #end if
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
33 #if $region and $region.__str__.strip() != '':
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
34 -r $region
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
35 #end if
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
36 $sv_only
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
37 </command>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
38 <inputs>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
39 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/>
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
40 <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
41 <!--
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
42 <param name="prefix" type="text" value="shear_sv" label="Prefix for all generated files">
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
43 <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator>
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
44 </param>
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
45 -->
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
46 <!-- reference data -->
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
47 <conditional name="genomeSource">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
48 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
49 <option value="indexed" selected="true">Use a cached reference genome</option>
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
50 <option value="history">Use fasta from the history</option>
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
51 <option value="svidx">Use SHEAR sv index from the history</option>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
52 </param>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
53 <when value="indexed">
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
54 <param name="ref_fastas" type="select" label="Select a reference genome fasta">
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
55 <options from_data_table="all_fasta">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
56 <filter type="sort_by" column="2" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
57 <validator type="no_options" message="No reference fasta files are available" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
58 </options>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
59 </param>
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
60 <param name="twobit_indices" type="select" label="Select the reference genome 2bit">
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
61 <options from_data_table="twobit">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
62 <filter type="sort_by" column="0" />
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
63 <!--
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
64 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
65 -->
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
66 <validator type="no_options" message="No indexes are available" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
67 </options>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
68 </param>
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
69 <param name="bwa_indices" type="select" label="Select the reference genome bwa indices">
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
70 <options from_data_table="bwa_indexes">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
71 <filter type="sort_by" column="2" />
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
72 <!--
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
73 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
1
a718ecb27e02 Comment out getting reference from history, need wrapper for that
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
74 -->
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
75 <validator type="no_options" message="No indexes are available" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
76 </options>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
77 </param>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
78 </when>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
79 <when value="history">
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
80 <param name="ref_fasta" type="data" format="fasta" label="Select a reference from history" />
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
81 <param name="save_svidx" type="boolean" truevalue="yes" falsevalue="no" label="Save sv generated reference indexes"/>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
82 </when>
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
83 <when value="svidx">
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
84 <param name="svidx" type="data" format="shear.svidx" label="Select a reference from history" />
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
85 </when>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
86 </conditional>
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
87 <param name="region" type="text" value="" optional="true" label="Region of the input alignment to analyze">
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
88 <help>"chr1" for full chromosome or "chr1:10000-15000" for a particular region, including endpoints).
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
89 Coordinates are 1-based.
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
90 </help>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
91 <validator type="regex" message="format: chr1:100-200">^\w+(:\d+-\d+)?$</validator>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
92 </param>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
93 <param name="sv_only" type="boolean" truevalue="--sv-only" falsevalue="" checked="false" label="SV Only prediction mode."
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
94 help="Will skip SNP/INDEL prediction and only return *.sdi and *.report results for SVs."/>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
95 </inputs>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
96 <stdio>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
97 <exit_code range="1:" level="fatal" description="Error" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
98 </stdio>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
99 <outputs>
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
100 <data format="txt" name="report_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.report" from_work_dir="shear_sv.snpindel.report">
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
101 <filter>sv_only == False</filter>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
102 </data>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
103 <data format="txt" name="report_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.report" from_work_dir="shear_sv.sv.report"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
104 <data format="txt" name="report_all" label="${tool.name} on ${on_string}: ${prefix}.all.report" from_work_dir="shear_sv.all.report">
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
105 <filter>sv_only == False</filter>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
106 </data>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
107 <data format="shear.sdi" name="sdi_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.sdi" from_work_dir="shear_sv.snpindel.sdi">
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
108 <filter>sv_only == False</filter>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
109 </data>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
110 <data format="shear.sdi" name="sdi_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.sdi" from_work_dir="shear_sv.sv.sdi"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
111 <data format="shear.sdi" name="sdi_all" label="${tool.name} on ${on_string}: ${prefix}.all.sdi" from_work_dir="shear_sv.all.sdi">
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
112 <filter>sv_only == False</filter>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
113 </data>
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
114 <data format="shear.svidx" name="sv_idx" label="${tool.name} on ${on_string}: ${prefix}.svidx">
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
115 <filter>genomeSource['refGenomeSource'] == 'history' and genomeSource['save_svidx'] == True</filter>
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
116 </data>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
117 </outputs>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
118 <tests>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
119 <test>
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
120 <param name="prefix" value="shear_test" />
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
121 <param name="bamfile" value="simulated-data.bam" ftype="bam" />
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
122 <param name="refGenomeSource" value="history"/>
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
123 <param name="ref_fasta" value="syn.fa" ftype="fasta" />
6
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
124 <param name="save_svidx" value="false"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
125 <param name="sv_only" value="true"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
126 <output name="sdi_sv" file="shear_sv.sdi"/>
0158f7356ffd Add new outputs and params to shear_sv.xml for version 2.3
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
127 <output name="report_sv" file="shear_sv.report"/>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
128 </test>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
129 </tests>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
130 <help>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
131 SHEAR-SV will process a BAM alignment file to find SVs and estimate the
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
132 heterogeneity level of those SVs. It will output a *.report file reporing the
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
133 SVs and their heterogeneity levels, and it will output a *.sdi file that can be
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
134 used for SHEAR-Assemble to reconstruct the new genome.
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
135 </help>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
136 </tool>