Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.xml @ 12:2656b09d2046 draft

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author galaxyp
date Mon, 30 Jan 2017 09:43:57 -0500
parents 982fb2cde6c5
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1 <tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
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2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
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3 <requirements>
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4 <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Job Failed" />
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8 </stdio>
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9 <command><![CDATA[
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10 Rscript --vanilla '$__tool_directory__/customProDB.R'
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11 --bam='$genome_annotation.bamInput'
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12 --bai='${genome_annotation.bamInput.metadata.bam_index}'
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13 --vcf='$genome_annotation.vcfInput'
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14 --rpkmCutoff=$rpkmCutoff
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15 --outputFile='${output_rpkm}'
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16
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17 #if str($genome_annotation.source) == 'history':
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18 --exon_anno='$genome_annotation.exonAnno'
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19 --proteinseq='$genome_annotation.proteinSeq'
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20 --procodingseq='$genome_annotation.proCodingSeq'
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21 --ids='$genome_annotation.ids'
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22 #if str($genome_annotation.dbsnpInCoding) != 'None':
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23 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
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24 #end if
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25 #if str($genome_annotation.cosmic) != 'None':
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26 --cosmic='$genome_annotation.cosmic"
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27 #end if
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28 #else:
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29 #set index_path = $genome_annotation.builtin.fields.path
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30 --exon_anno='$index_path/exon_anno.RData'
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31 --proteinseq='$index_path/proseq.RData'
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32 --procodingseq='$index_path/procodingseq.RData'
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33 --ids='$index_path/ids.RData'
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34 #if $genome_annotation.dbsnpInCoding:
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35 --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
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36 #end if
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37 #if $genome_annotation.cosmic:
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38 --cosmic='$index_path/cosmic.RData'
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39 #end if
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40 #end if
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41 2>1
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42 ]]>
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43 </command>
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44 <inputs>
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45 <conditional name="genome_annotation">
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46 <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
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47 <option value="builtin">Use a built-in genome annotation</option>
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48 <option value="history">Use annotation from your history</option>
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49 </param>
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50 <when value="builtin">
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51 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
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52 <options from_data_table="customProDB">
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53 <filter type="sort_by" column="2"/>
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54 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
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55 </options>
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56 </param>
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57 <param name="bamInput" type="data" format="bam" label="BAM file">
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58 <validator type="unspecified_build" />
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59 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
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60 </param>
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61 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
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62 <validator type="unspecified_build" />
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63 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
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64 </param>-->
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65 <param name="vcfInput" type="data" format="vcf" label="VCF file">
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66 <validator type="unspecified_build" />
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67 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
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68 </param>
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69 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
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70 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
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71 </when>
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72 <when value="history">
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73 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
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74 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
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75 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
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76 <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
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77 <param name="bamInput" type="data" format="bam" label="BAM file">
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78 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
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79 </param>
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80 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
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81 <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
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82 </param>-->
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83 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
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84 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
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85 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
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86 </when>
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87 </conditional>
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88 <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
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89 </inputs>
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90 <outputs>
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91 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
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92 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
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93 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
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98 <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
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99 <param name="source" value="history" />
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100 <param name="exonAnno" value="exon_anno.RData" />
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101 <param name="proteinSeq" value="proseq.RData" />
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102 <param name="proCodingSeq" value="procodingseq.RData" />
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103 <param name="ids" value="ids.RData" />
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104 <output name="output_rpkm" file="test_rpkm.fasta" />
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105 <output name="output_snv" file="test_snv.fasta" />
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106 <output name="output_indel" file="test_indel.fasta" />
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107 </test>
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108 </tests>
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109 <help><![CDATA[
11
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110 **Description**
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111
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112 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
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113
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114 ]]></help>
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115 <citations>
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116 <citation type="doi">10.1093/bioinformatics/btt543</citation>
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117 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub
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118 repository},
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119 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
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120 {$sha1$}" -->
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121 </citations>
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122 </tool>