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comparison customProDB.xml @ 6:61e45c111ef7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 03 Feb 2016 12:37:47 -0500
parents 6db27bef602f
children b83a4002aab1
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5:6db27bef602f 6:61e45c111ef7
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 </stdio> 5 </stdio>
6 <command interpreter="Rscript --vanilla">customProDB.R 6 <command interpreter="Rscript --vanilla">customProDB.R
7 7
8 --bam="$bamInput" 8 --bam="$genome_annotation.bamInput"
9 --vcf="$vcfInput" 9 --bai="${genome_annotation.bamInput.metadata.bam_index}"
10 --outputFile="$output" 10 --vcf="$genome_annotation.vcfInput"
11 --outputFile="${output_rpkm}"
11 12
12 #if str($genome_annotation.source) == "history": 13 #if str($genome_annotation.source) == "history":
13 --exon_anno="$genome_annotation.exonAnno" 14 --exon_anno="$genome_annotation.exonAnno"
14 --proteinseq="$genome_annotation.proteinSeq" 15 --proteinseq="$genome_annotation.proteinSeq"
15 --procodingseq="$genome_annotation.proCodingSeq" 16 --procodingseq="$genome_annotation.proCodingSeq"
17 --ids="$genome_annotation.ids"
16 #else: 18 #else:
17 #set index_path = $genome_annotation.builtin.fields.path 19 #set index_path = $genome_annotation.builtin.fields.path
18 --exon_anno="$index_path/exon_anno.RData" 20 --exon_anno="$index_path/exon_anno.RData"
19 --proteinseq="$index_path/proseq.RData" 21 --proteinseq="$index_path/proseq.RData"
20 --procodingseq="$index_path/procodingseq.RData" 22 --procodingseq="$index_path/procodingseq.RData"
23 --ids="$index_path/ids.RData"
21 #end if 24 #end if
22 25
23 2&gt;&amp;1</command> 26 2&gt;&amp;1</command>
24 <inputs> 27 <inputs>
25 <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
26 <validator type="empty_field" message="This field is required."/>
27 </param>
28 <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
29 <validator type="empty_field" message="This field is required."/>
30 </param>
31
32 <conditional name="genome_annotation"> 28 <conditional name="genome_annotation">
33 <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"> 29 <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">
34 <option value="builtin">Use a built-in genome annotation</option> 30 <option value="builtin">Use a built-in genome annotation</option>
35 <option value="history">Use a genome from the history and build index</option> 31 <option value="history">Use annotation from your history</option>
36 </param> 32 </param>
37 <when value="builtin"> 33 <when value="builtin">
38 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team"> 34 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
39 <options from_data_table="customProDB"> 35 <options from_data_table="customProDB">
40 <filter type="sort_by" column="2"/> 36 <filter type="sort_by" column="2"/>
41 <validator type="no_options" message="No annotations are available for the selected input dataset"/> 37 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
42 </options> 38 </options>
43 </param> 39 </param>
40 <param name="bamInput" type="data" format="bam" label="BAM file">
41 <validator type="unspecified_build" />
42 <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" />
43 </param>
44 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
45 <validator type="unspecified_build" />
46 <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" />
47 </param>-->
48 <param name="vcfInput" type="data" format="vcf" label="VCF file">
49 <validator type="unspecified_build" />
50 <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" />
51 </param>
44 </when> 52 </when>
45 <when value="history"> 53 <when value="history">
46 <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" /> 54 <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
47 <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" /> 55 <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
48 <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" /> 56 <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
57 <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
58 <param name="bamInput" type="data" format="bam" label="BAM file">
59 <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" />
60 </param>
61 <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
62 <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" />
63 </param>
64 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
49 </when> 65 </when>
50 </conditional> 66 </conditional>
51 </inputs> 67 </inputs>
52 <outputs> 68 <outputs>
53 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/> 69 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
70 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
71 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
54 </outputs> 72 </outputs>
55 <!--<tests> 73 <tests>
56 <test> 74 <test>
57 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" /> 75 <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
58 <param name="scoreColumn" value="Myrimatch:MVH" /> 76 <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
59 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" /> 77 <param name="source" value="history" />
78 <param name="exonAnno" value="exon_anno.RData" />
79 <param name="proteinSeq" value="proseq.RData" />
80 <param name="proCodingSeq" value="procodingseq.RData" />
81 <param name="ids" value="ids.RData" />
82 <output name="output_rpkm" file="test_rpkm.fasta" />
83 <output name="output_snv" file="test_snv.fasta" />
84 <output name="output_indel" file="test_indel.fasta" />
60 </test> 85 </test>
61 <test> 86 </tests>
62 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
63 <param name="scoreColumn" value="Myrimatch:MVH" />
64 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
65 </test>
66 </tests>-->
67 <help> 87 <help>
68 **Description** 88 **Description**
69 89
70 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). 90 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
71 </help> 91 </help>