Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.xml @ 4:bc08158abf77 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6
author galaxyp
date Thu, 08 Jun 2017 11:06:13 -0400
parents 344f606eeb9a
children 2c7df0077d28
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bc08158abf77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6
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1 <tool id="custom_pro_db" name="CustomProDB" version="1.16.1.0">
0
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2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
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3 <requirements>
1
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4 <requirement type="package" version="3.3.1">r-base</requirement>
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5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
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6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
1
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7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
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8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
4
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9 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
1
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10 <requirement type="package" version="1.11.1">r-devtools</requirement>
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11 <requirement type="package" version="3.98_1.4">r-xml</requirement>
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12 <requirement type="package" version="0.10.11">r-rmysql</requirement>
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13 <requirement type="package" version="1.0.2">r-testthat</requirement>
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14 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
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15 <requirement type="package" version="1.1.2">r-stringi</requirement>
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16 <requirement type="package" version="1.1.0">r-stringr</requirement>
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17 <requirement type="package" version="1.10.0">r-data.table</requirement>
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18 <requirement type="package" version="0.4_10">r-sqldf</requirement>
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19 <requirement type="package" version="0.6_6">r-gsubfn</requirement>
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20 <requirement type="package" version="2.3_47">r-chron</requirement>
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21 <requirement type="package" version="0.3_10">r-proto</requirement>
1
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22 <requirement type="package" version="1.8.4">r-plyr</requirement>
0
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23 </requirements>
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24 <stdio>
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25 <exit_code range="1:" level="fatal" description="Job Failed" />
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26 </stdio>
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27 <command><![CDATA[
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28 Rscript --vanilla '$__tool_directory__/customProDB.R'
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29 --bam='$genome_annotation.bamInput'
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30 --bai='${genome_annotation.bamInput.metadata.bam_index}'
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31 --vcf='$genome_annotation.vcfInput'
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32 --rpkmCutoff=$rpkmCutoff
1
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33 $outputIndels
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34 $outputSQLite
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35 $outputRData
0
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36
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37 #if str($genome_annotation.source) == 'history':
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38 --exon_anno='$genome_annotation.exonAnno'
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39 --proteinseq='$genome_annotation.proteinSeq'
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40 --procodingseq='$genome_annotation.proCodingSeq'
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41 --ids='$genome_annotation.ids'
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42 #if str($genome_annotation.dbsnpInCoding) != 'None':
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43 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
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44 #end if
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45 #if str($genome_annotation.cosmic) != 'None':
1
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46 --cosmic='$genome_annotation.cosmic'
0
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47 #end if
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48 #else:
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49 #set index_path = $genome_annotation.builtin.fields.path
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50 --exon_anno='$index_path/exon_anno.RData'
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51 --proteinseq='$index_path/proseq.RData'
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52 --procodingseq='$index_path/procodingseq.RData'
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53 --ids='$index_path/ids.RData'
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54 #if $genome_annotation.dbsnpInCoding:
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55 --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
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56 #end if
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57 #if $genome_annotation.cosmic:
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58 --cosmic='$index_path/cosmic.RData'
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59 #end if
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60 #end if
2
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61 2>&1
0
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62 ]]>
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63 </command>
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64 <inputs>
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65 <conditional name="genome_annotation">
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66 <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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67 <option value="builtin">Use a built-in genome annotation</option>
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68 <option value="history">Use annotation from your history</option>
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69 </param>
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70 <when value="builtin">
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71 <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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72 <options from_data_table="customProDB">
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73 <filter type="sort_by" column="2"/>
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74 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
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75 </options>
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76 </param>
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77 <param name="bamInput" type="data" format="bam" label="BAM file">
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78 <validator type="unspecified_build" />
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79 <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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80 </param>
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81 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
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82 <validator type="unspecified_build" />
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83 <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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84 </param>-->
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85 <param name="vcfInput" type="data" format="vcf" label="VCF file">
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86 <validator type="unspecified_build" />
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87 <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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88 </param>
4
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89 <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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90 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" help="The genome annotation must have been prepared with COSMIC." />
0
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91 </when>
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92 <when value="history">
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93 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
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94 <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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95 <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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96 <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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97 <param name="bamInput" type="data" format="bam" label="BAM file">
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98 <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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99 </param>
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100 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
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101 <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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102 </param>-->
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103 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
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104 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
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105 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
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106 </when>
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107 </conditional>
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108 <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." />
1
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109 <param name="outputIndels" type="boolean" truevalue="--outputIndels" falsevalue="" label="Create a variant FASTA for short insertions and deletions" />
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110 <param name="outputSQLite" type="boolean" truevalue="--outputSQLite" falsevalue="" label="Create SQLite files for mapping proteins to genome and summarizing variant proteins" />
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111 <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" />
0
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112 </inputs>
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113 <outputs>
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114 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
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115 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
1
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116 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta">
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117 <filter>outputIndels is True</filter>
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118 </data>
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119 <data format="rdata" name="output_variant_annotation_rdata" from_work_dir="output.rdata" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.RData">
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120 <filter>outputRData is True</filter>
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121 </data>
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122 <data format="sqlite" name="output_genomic_mapping_sqlite" from_work_dir="output_genomic_mapping.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_genomicMapping.sqlite">
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123 <filter>outputSQLite is True</filter>
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124 </data>
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125 <data format="sqlite" name="output_variant_annotation_sqlite" from_work_dir="output_variant_annotation.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.sqlite">
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126 <filter>outputSQLite is True</filter>
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127 </data>
0
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128 </outputs>
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129 <tests>
1
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130 <test expect_num_outputs="5">
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131 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
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132 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
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133 <param name="source" value="history" />
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134 <param name="exonAnno" value="hg19/exon_anno.RData" />
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135 <param name="proteinSeq" value="hg19/proseq.RData" />
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136 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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137 <param name="ids" value="hg19/ids.RData" />
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138 <param name="rpkmCutoff" value="1" />
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139 <param name="outputIndels" value="" />
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140 <param name="outputRData" value="--outputRData" />
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141 <param name="outputSQLite" value="--outputSQLite" />
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142 <output name="output_rpkm" file="hg19_rpkm1.fasta" />
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143 <output name="output_snv" file="hg19_snv.fasta" />
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144 <output name="output_variant_annotation_rdata" file="hg19_variant_annotation.rdata" />
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145 <output name="output_genomic_mapping_sqlite" file="hg19_genomic_mapping.sqlite" />
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146 <output name="output_variant_annotation_sqlite" file="hg19_variant_annotation.sqlite" />
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147 </test>
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148 <test expect_num_outputs="5">
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149 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
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150 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
0
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151 <param name="source" value="history" />
1
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152 <param name="exonAnno" value="hg19/exon_anno.RData" />
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153 <param name="proteinSeq" value="hg19/proseq.RData" />
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154 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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155 <param name="ids" value="hg19/ids.RData" />
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156 <param name="dbsnpInCoding" value="hg19/dbsnpinCoding.RData" />
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157 <param name="cosmic" value="hg19/cosmic.RData" />
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158 <param name="rpkmCutoff" value="0" />
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159 <param name="outputIndels" value="--outputIndels" />
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160 <param name="outputSQLite" value="--outputSQLite" />
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161 <output name="output_rpkm" file="hg19_rpkm0.fasta" />
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162 <output name="output_snv" file="hg19_dbsnp_snv.fasta" />
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163 <output name="output_indel" file="hg19_indel.fasta" />
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164 <output name="output_variant_annotation_rdata" file="hg19_dbsnp_variant_annotation.rdata" />
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165 <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" />
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166 </test>
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167 <test expect_num_outputs="3">
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168 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
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169 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
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170 <param name="source" value="history" />
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171 <param name="exonAnno" value="hg19/exon_anno.RData" />
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172 <param name="proteinSeq" value="hg19/proseq.RData" />
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173 <param name="proCodingSeq" value="hg19/procodingseq.RData" />
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174 <param name="ids" value="hg19/ids.RData" />
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175 <param name="rpkmCutoff" value="1000" />
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176 <param name="outputIndels" value="--outputIndels" />
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177 <output name="output_rpkm" file="hg19_rpkm1000.fasta" />
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178 <output name="output_snv" file="hg19_snv.fasta" />
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179 <output name="output_indel" file="hg19_indel.fasta" />
0
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180 </test>
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181 </tests>
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182 <help>
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183 **Description**
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184
4
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185 Generate custom protein FASTAs from exosome or transcriptome data.
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186
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187 The reference protein set can be filtered by transcript expression level (RPKM calculated from a BAM file),
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188 and variant protein forms can be predicted based on variant calls (SNPs and INDELs reported in a VCF file).
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189
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190
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191 **Annotations**
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192 CustomProDB depends on a set of annotation files (in RData format) to create reference and variant protein sequences.
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193 Galaxy administrators can use the customProDB data manager to create these annotations to make them available for users.
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194 </help>
0
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195 <citations>
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196 <citation type="doi">10.1093/bioinformatics/btt543</citation>
1
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197 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
0
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198 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
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199 {$sha1$}" -->
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200 </citations>
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201 </tool>