Mercurial > repos > jjohnson > shear
annotate shear_sv.xml @ 11:13d4d1d1da6a default tip
Update to latest changeset for package_samtools_0_1_18
| author | Jim Johnson <jj@umn.edu> |
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| date | Fri, 08 Nov 2013 09:37:57 -0600 |
| parents | 2620f7984418 |
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| rev | line source |
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| 0 | 1 <?xml version="1.0"?> |
| 10 | 2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.5"> |
| 0 | 3 <description>find SVs and estimate the heterogeneity levels from a BAM</description> |
| 4 <requirements> | |
| 10 | 5 <requirement type="package" version="0.2.5">shear</requirement> |
| 0 | 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> | |
| 10 | 9 <requirement type="package" version="latest">blat_server</requirement> |
| 9 | 10 <requirement type="package" version="3">cap3</requirement> |
| 0 | 11 </requirements> |
| 12 <!-- | |
| 13 <version_command></version_command> | |
| 14 --> | |
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15 <command interpreter="python"> |
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16 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command sv |
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17 -p $prefix ## used in gerenating ouput file names |
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18 -b $bamfile |
| 0 | 19 #if $genomeSource.refGenomeSource == 'indexed': |
| 20 -f $genomeSource.ref_fastas.fields.path | |
| 21 -i $genomeSource.bwa_indices.fields.path | |
| 3 | 22 -t $genomeSource.twobit_indices.fields.path |
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23 #elif $genomeSource.refGenomeSource == 'svidx': |
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24 -f $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa |
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25 -i $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa |
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26 -t $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.2bit |
| 0 | 27 #else: |
| 28 -f $genomeSource.ref_fasta | |
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29 #if $genomeSource.save_svidx: |
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30 -D $sv_idx.extra_files_path |
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31 #end if |
| 0 | 32 #end if |
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33 #if $region and $region.__str__.strip() != '': |
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34 -r $region |
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35 #end if |
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36 $sv_only |
| 0 | 37 </command> |
| 38 <inputs> | |
| 39 <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> | |
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40 <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/> |
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41 <!-- |
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42 <param name="prefix" type="text" value="shear_sv" label="Prefix for all generated files"> |
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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> |
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44 </param> |
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45 --> |
| 0 | 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> | |
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50 <option value="history">Use fasta from the history</option> |
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51 <option value="svidx">Use SHEAR sv index from the history</option> |
| 0 | 52 </param> |
| 53 <when value="indexed"> | |
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54 <param name="ref_fastas" type="select" label="Select a reference genome fasta"> |
| 0 | 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> | |
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60 <param name="twobit_indices" type="select" label="Select the reference genome 2bit"> |
| 0 | 61 <options from_data_table="twobit"> |
| 62 <filter type="sort_by" column="0" /> | |
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63 <!-- |
| 0 | 64 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
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65 --> |
| 0 | 66 <validator type="no_options" message="No indexes are available" /> |
| 67 </options> | |
| 68 </param> | |
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69 <param name="bwa_indices" type="select" label="Select the reference genome bwa indices"> |
| 0 | 70 <options from_data_table="bwa_indexes"> |
| 71 <filter type="sort_by" column="2" /> | |
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72 <!-- |
| 0 | 73 <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" /> |
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74 --> |
| 0 | 75 <validator type="no_options" message="No indexes are available" /> |
| 76 </options> | |
| 77 </param> | |
| 78 </when> | |
| 79 <when value="history"> | |
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80 <param name="ref_fasta" type="data" format="fasta" label="Select a reference from history" /> |
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81 <param name="save_svidx" type="boolean" truevalue="yes" falsevalue="no" label="Save sv generated reference indexes"/> |
| 0 | 82 </when> |
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83 <when value="svidx"> |
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84 <param name="svidx" type="data" format="shear.svidx" label="Select a reference from history" /> |
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85 </when> |
| 0 | 86 </conditional> |
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87 <param name="region" type="text" value="" optional="true" label="Region of the input alignment to analyze"> |
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88 <help>"chr1" for full chromosome or "chr1:10000-15000" for a particular region, including endpoints). |
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89 Coordinates are 1-based. |
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90 </help> |
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91 <validator type="regex" message="format: chr1:100-200">^\w+(:\d+-\d+)?$</validator> |
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92 </param> |
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93 <param name="sv_only" type="boolean" truevalue="--sv-only" falsevalue="" checked="false" label="SV Only prediction mode." |
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94 help="Will skip SNP/INDEL prediction and only return *.sdi and *.report results for SVs."/> |
| 0 | 95 </inputs> |
| 96 <stdio> | |
| 97 <exit_code range="1:" level="fatal" description="Error" /> | |
| 98 </stdio> | |
| 99 <outputs> | |
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100 <data format="txt" name="report_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.report" from_work_dir="shear_sv.snpindel.report"> |
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101 <filter>sv_only == False</filter> |
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102 </data> |
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103 <data format="txt" name="report_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.report" from_work_dir="shear_sv.sv.report"/> |
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104 <data format="txt" name="report_all" label="${tool.name} on ${on_string}: ${prefix}.all.report" from_work_dir="shear_sv.all.report"> |
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105 <filter>sv_only == False</filter> |
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106 </data> |
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107 <data format="shear.sdi" name="sdi_snpindel" label="${tool.name} on ${on_string}: ${prefix}.snpindel.sdi" from_work_dir="shear_sv.snpindel.sdi"> |
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108 <filter>sv_only == False</filter> |
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109 </data> |
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110 <data format="shear.sdi" name="sdi_sv" label="${tool.name} on ${on_string}: ${prefix}.sv.sdi" from_work_dir="shear_sv.sv.sdi"/> |
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111 <data format="shear.sdi" name="sdi_all" label="${tool.name} on ${on_string}: ${prefix}.all.sdi" from_work_dir="shear_sv.all.sdi"> |
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112 <filter>sv_only == False</filter> |
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113 </data> |
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114 <data format="shear.svidx" name="sv_idx" label="${tool.name} on ${on_string}: ${prefix}.svidx"> |
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115 <filter>genomeSource['refGenomeSource'] == 'history' and genomeSource['save_svidx'] == True</filter> |
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116 </data> |
| 0 | 117 </outputs> |
| 118 <tests> | |
| 119 <test> | |
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120 <param name="prefix" value="shear_test" /> |
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121 <param name="bamfile" value="simulated-data.bam" ftype="bam" /> |
| 0 | 122 <param name="refGenomeSource" value="history"/> |
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123 <param name="ref_fasta" value="syn.fa" ftype="fasta" /> |
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124 <param name="save_svidx" value="false"/> |
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125 <param name="sv_only" value="true"/> |
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126 <output name="sdi_sv" file="shear_sv.sdi"/> |
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127 <output name="report_sv" file="shear_sv.report"/> |
| 0 | 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> |