Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.xml @ 19:14b5405f898a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30
author galaxyp
date Fri, 22 Feb 2019 02:12:57 -0500
parents c429c2baecb8
children
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14b5405f898a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30
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1 <tool id="custom_pro_db" name="CustomProDB" version="1.22.0">
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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="1.22.0">bioconductor-customprodb</requirement>-->
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5 <requirement type="package" version="1.26.0">bioconductor-rgalaxy</requirement>
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6 <requirement type="package" version="1.28.3">bioconductor-variantannotation</requirement>
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7 <requirement type="package" version="2.0.1">r-devtools</requirement>
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8 <requirement type="package" version="2.0.1">r-testthat</requirement>
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9 <requirement type="package" version="0.1.7">r-getoptlong</requirement>
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10 <requirement type="package" version="1.12.0">r-data.table</requirement>
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11 <requirement type="package" version="0.4_11">r-sqldf</requirement>
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12 <requirement type="package" version="1.8.4">r-plyr</requirement>
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13 <requirement type="package" version="0.10.13">r-rmysql</requirement>
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14 </requirements>
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15 <stdio>
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16 <exit_code range="1:" level="fatal" description="Job Failed" />
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17 </stdio>
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18 <command><![CDATA[
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19 Rscript --vanilla '$__tool_directory__/customProDB.R'
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20 --bam='$genome_annotation.bamInput'
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21 --bai='${genome_annotation.bamInput.metadata.bam_index}'
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22 --vcf='$genome_annotation.vcfInput'
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23 --rpkmCutoff=$rpkmCutoff
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24 $outputIndels
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25 $outputSQLite
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26 $outputRData
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27
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28 #if str($genome_annotation.source) == 'history':
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29 --exon_anno='$genome_annotation.exonAnno'
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30 --proteinseq='$genome_annotation.proteinSeq'
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31 --procodingseq='$genome_annotation.proCodingSeq'
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32 --ids='$genome_annotation.ids'
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33 #if str($genome_annotation.dbsnpInCoding) != 'None':
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34 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
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35 #end if
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36 #if str($genome_annotation.cosmic) != 'None':
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37 --cosmic='$genome_annotation.cosmic'
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38 #end if
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39 #else:
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40 #set index_path = $genome_annotation.builtin.fields.path
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41 --exon_anno='$index_path/exon_anno.RData'
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42 --proteinseq='$index_path/proseq.RData'
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43 --procodingseq='$index_path/procodingseq.RData'
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44 --ids='$index_path/ids.RData'
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45 #if $genome_annotation.dbsnpInCoding:
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46 --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
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47 #end if
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48 #if $genome_annotation.cosmic:
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49 --cosmic='$index_path/cosmic.RData'
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50 #end if
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51 #end if
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52 2>&1
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53 ]]>
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54 </command>
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55 <inputs>
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56 <conditional name="genome_annotation">
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57 <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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58 <option value="builtin">Use a built-in genome annotation</option>
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59 <option value="history">Use annotation from your history</option>
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60 </param>
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61 <when value="builtin">
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62 <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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63 <options from_data_table="customProDB">
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64 <filter type="sort_by" column="2"/>
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65 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
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66 </options>
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67 </param>
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68 <param name="bamInput" type="data" format="bam" label="BAM file">
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69 <validator type="unspecified_build" />
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70 <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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71 </param>
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72 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
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73 <validator type="unspecified_build" />
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74 <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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75 </param>-->
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76 <param name="vcfInput" type="data" format="vcf" label="VCF file">
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77 <validator type="unspecified_build" />
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78 <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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79 </param>
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80 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP" help="The genome annotation must have been prepared with dbSNP." />
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81 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" help="The genome annotation must have been prepared with COSMIC." />
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82 </when>
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83 <when value="history">
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84 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
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85 <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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86 <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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87 <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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88 <param name="bamInput" type="data" format="bam" label="BAM file">
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89 <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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90 </param>
12
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91 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
11
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92 <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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93 </param>-->
11
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94 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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95 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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96 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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97 </when>
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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98 </conditional>
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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99 <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." />
14
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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100 <param name="outputIndels" type="boolean" truevalue="--outputIndels" falsevalue="" label="Create a variant FASTA for short insertions and deletions" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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101 <param name="outputSQLite" type="boolean" truevalue="--outputSQLite" falsevalue="" label="Create SQLite files for mapping proteins to genome and summarizing variant proteins" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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102 <param name="outputRData" type="boolean" truevalue="--outputRData" falsevalue="" label="Create RData file of variant protein coding sequences" help="The PSM2SAM tool needs this to map variant proteins to genomic locations" />
11
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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103 </inputs>
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104 <outputs>
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105 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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106 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
14
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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107 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta">
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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108 <filter>outputIndels is True</filter>
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109 </data>
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110 <data format="rdata" name="output_variant_annotation_rdata" from_work_dir="output.rdata" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.RData">
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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111 <filter>outputRData is True</filter>
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112 </data>
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113 <data format="sqlite" name="output_genomic_mapping_sqlite" from_work_dir="output_genomic_mapping.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_genomicMapping.sqlite">
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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114 <filter>outputSQLite is True</filter>
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115 </data>
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116 <data format="sqlite" name="output_variant_annotation_sqlite" from_work_dir="output_variant_annotation.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.sqlite">
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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117 <filter>outputSQLite is True</filter>
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118 </data>
11
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119 </outputs>
982fb2cde6c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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120 <tests>
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121 <test expect_num_outputs="5">
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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122 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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123 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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124 <param name="source" value="history" />
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125 <param name="exonAnno" value="hg19/exon_anno.RData" />
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126 <param name="proteinSeq" value="hg19/proseq.RData" />
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127 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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128 <param name="ids" value="hg19/ids.RData" />
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129 <param name="rpkmCutoff" value="1" />
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130 <param name="outputIndels" value="" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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131 <param name="outputRData" value="--outputRData" />
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132 <param name="outputSQLite" value="--outputSQLite" />
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133 <output name="output_rpkm" file="hg19_rpkm1.fasta" />
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134 <output name="output_snv" file="hg19_snv.fasta" />
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135 <output name="output_variant_annotation_rdata" file="hg19_variant_annotation.rdata" />
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136 <output name="output_genomic_mapping_sqlite" file="hg19_genomic_mapping.sqlite" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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137 <output name="output_variant_annotation_sqlite" file="hg19_variant_annotation.sqlite" />
bc10f130dbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
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138 </test>
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139 <test expect_num_outputs="5">
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140 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
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141 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
11
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142 <param name="source" value="history" />
14
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143 <param name="exonAnno" value="hg19/exon_anno.RData" />
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144 <param name="proteinSeq" value="hg19/proseq.RData" />
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145 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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146 <param name="ids" value="hg19/ids.RData" />
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147 <param name="dbsnpInCoding" value="hg19/dbsnpinCoding.RData" />
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148 <param name="cosmic" value="hg19/cosmic.RData" />
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149 <param name="rpkmCutoff" value="0" />
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150 <param name="outputIndels" value="--outputIndels" />
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151 <param name="outputSQLite" value="--outputSQLite" />
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152 <output name="output_rpkm" file="hg19_rpkm0.fasta" />
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153 <output name="output_snv" file="hg19_dbsnp_snv.fasta" />
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154 <output name="output_indel" file="hg19_indel.fasta" />
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155 <output name="output_genomic_mapping_sqlite" file="hg19_dbsnp_genomic_mapping.sqlite" />
14
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156 <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" />
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157 </test>
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158 <test expect_num_outputs="3">
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159 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
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160 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
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161 <param name="source" value="history" />
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162 <param name="exonAnno" value="hg19/exon_anno.RData" />
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163 <param name="proteinSeq" value="hg19/proseq.RData" />
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164 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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165 <param name="ids" value="hg19/ids.RData" />
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166 <param name="rpkmCutoff" value="1000" />
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167 <param name="outputIndels" value="--outputIndels" />
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168 <output name="output_rpkm" file="hg19_rpkm1000.fasta" />
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169 <output name="output_snv" file="hg19_snv.fasta" />
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170 <output name="output_indel" file="hg19_indel.fasta" />
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171 </test>
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172 </tests>
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173 <help>
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174 **Description**
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175
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176 Generate custom protein FASTAs from exosome or transcriptome data.
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177
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178 The reference protein set can be filtered by transcript expression level (RPKM calculated from a BAM file),
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179 and variant protein forms can be predicted based on variant calls (SNPs and INDELs reported in a VCF file).
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180
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181
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182 **Annotations**
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183 CustomProDB depends on a set of annotation files (in RData format) to create reference and variant protein sequences.
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184 Galaxy administrators can use the customProDB data manager to create these annotations to make them available for users.
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185 </help>
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186 <citations>
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187 <citation type="doi">10.1093/bioinformatics/btt543</citation>
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188 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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189 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
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190 {$sha1$}" -->
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191 </citations>
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192 </tool>