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comparison shear_sv.xml @ 0:65255beda972

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author jjohnson
date Fri, 08 Nov 2013 16:23:10 -0500
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1 <?xml version="1.0"?>
2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.5">
3 <description>find SVs and estimate the heterogeneity levels from a BAM</description>
4 <requirements>
5 <requirement type="package" version="0.2.5">shear</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="0.6.2">bwa</requirement>
8 <requirement type="package" version="1.0.1">crest</requirement>
9 <requirement type="package" version="latest">blat_server</requirement>
10 <requirement type="package" version="3">cap3</requirement>
11 </requirements>
12 <!--
13 <version_command></version_command>
14 -->
15 <command interpreter="python">
16 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command sv
17 -p $prefix ## used in gerenating ouput file names
18 -b $bamfile
19 #if $genomeSource.refGenomeSource == 'indexed':
20 -f $genomeSource.ref_fastas.fields.path
21 -i $genomeSource.bwa_indices.fields.path
22 -t $genomeSource.twobit_indices.fields.path
23 #elif $genomeSource.refGenomeSource == 'svidx':
24 -f $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
25 -i $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
26 -t $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.2bit
27 #else:
28 -f $genomeSource.ref_fasta
29 #if $genomeSource.save_svidx:
30 -D $sv_idx.extra_files_path
31 #end if
32 #end if
33 #if $region and $region.__str__.strip() != '':
34 -r $region
35 #end if
36 $sv_only
37 </command>
38 <inputs>
39 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/>
40 <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
41 <!--
42 <param name="prefix" type="text" value="shear_sv" label="Prefix for all generated files">
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>
44 </param>
45 -->
46 <!-- reference data -->
47 <conditional name="genomeSource">
48 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
49 <option value="indexed" selected="true">Use a cached reference genome</option>
50 <option value="history">Use fasta from the history</option>
51 <option value="svidx">Use SHEAR sv index from the history</option>
52 </param>
53 <when value="indexed">
54 <param name="ref_fastas" type="select" label="Select a reference genome fasta">
55 <options from_data_table="all_fasta">
56 <filter type="sort_by" column="2" />
57 <validator type="no_options" message="No reference fasta files are available" />
58 </options>
59 </param>
60 <param name="twobit_indices" type="select" label="Select the reference genome 2bit">
61 <options from_data_table="twobit">
62 <filter type="sort_by" column="0" />
63 <!--
64 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
65 -->
66 <validator type="no_options" message="No indexes are available" />
67 </options>
68 </param>
69 <param name="bwa_indices" type="select" label="Select the reference genome bwa indices">
70 <options from_data_table="bwa_indexes">
71 <filter type="sort_by" column="2" />
72 <!--
73 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
74 -->
75 <validator type="no_options" message="No indexes are available" />
76 </options>
77 </param>
78 </when>
79 <when value="history">
80 <param name="ref_fasta" type="data" format="fasta" label="Select a reference from history" />
81 <param name="save_svidx" type="boolean" truevalue="yes" falsevalue="no" label="Save sv generated reference indexes"/>
82 </when>
83 <when value="svidx">
84 <param name="svidx" type="data" format="shear.svidx" label="Select a reference from history" />
85 </when>
86 </conditional>
87 <param name="region" type="text" value="" optional="true" label="Region of the input alignment to analyze">
88 <help>"chr1" for full chromosome or "chr1:10000-15000" for a particular region, including endpoints).
89 Coordinates are 1-based.
90 </help>
91 <validator type="regex" message="format: chr1:100-200">^\w+(:\d+-\d+)?$</validator>
92 </param>
93 <param name="sv_only" type="boolean" truevalue="--sv-only" falsevalue="" checked="false" label="SV Only prediction mode."
94 help="Will skip SNP/INDEL prediction and only return *.sdi and *.report results for SVs."/>
95 </inputs>
96 <stdio>
97 <exit_code range="1:" level="fatal" description="Error" />
98 </stdio>
99 <outputs>
100 <data format="txt" name="report_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.report" from_work_dir="shear_sv.snpindel.report">
101 <filter>sv_only == False</filter>
102 </data>
103 <data format="txt" name="report_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.report" from_work_dir="shear_sv.sv.report"/>
104 <data format="txt" name="report_all" label="${tool.name} on ${on_string}: ${prefix}.all.report" from_work_dir="shear_sv.all.report">
105 <filter>sv_only == False</filter>
106 </data>
107 <data format="shear.sdi" name="sdi_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.sdi" from_work_dir="shear_sv.snpindel.sdi">
108 <filter>sv_only == False</filter>
109 </data>
110 <data format="shear.sdi" name="sdi_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.sdi" from_work_dir="shear_sv.sv.sdi"/>
111 <data format="shear.sdi" name="sdi_all" label="${tool.name} on ${on_string}: ${prefix}.all.sdi" from_work_dir="shear_sv.all.sdi">
112 <filter>sv_only == False</filter>
113 </data>
114 <data format="shear.svidx" name="sv_idx" label="${tool.name} on ${on_string}: ${prefix}.svidx">
115 <filter>genomeSource['refGenomeSource'] == 'history' and genomeSource['save_svidx'] == True</filter>
116 </data>
117 </outputs>
118 <tests>
119 <test>
120 <param name="prefix" value="shear_test" />
121 <param name="bamfile" value="simulated-data.bam" ftype="bam" />
122 <param name="refGenomeSource" value="history"/>
123 <param name="ref_fasta" value="syn.fa" ftype="fasta" />
124 <param name="save_svidx" value="false"/>
125 <param name="sv_only" value="true"/>
126 <output name="sdi_sv" file="shear_sv.sdi"/>
127 <output name="report_sv" file="shear_sv.report"/>
128 </test>
129 </tests>
130 <help>
131 SHEAR-SV will process a BAM alignment file to find SVs and estimate the
132 heterogeneity level of those SVs. It will output a *.report file reporing the
133 SVs and their heterogeneity levels, and it will output a *.sdi file that can be
134 used for SHEAR-Assemble to reconstruct the new genome.
135 </help>
136 </tool>