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comparison customProDB.xml @ 0:8ccfff69dd57 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
author galaxyp
date Tue, 14 Mar 2017 14:14:38 -0400
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1 <tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
3 <requirements>
4 <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Job Failed" />
9 </stdio>
10 <command><![CDATA[
11 Rscript --vanilla '$__tool_directory__/customProDB.R'
12 --bam='$genome_annotation.bamInput'
13 --bai='${genome_annotation.bamInput.metadata.bam_index}'
14 --vcf='$genome_annotation.vcfInput'
15 --rpkmCutoff=$rpkmCutoff
16 --outputFile='${output_rpkm}'
17
18 #if str($genome_annotation.source) == 'history':
19 --exon_anno='$genome_annotation.exonAnno'
20 --proteinseq='$genome_annotation.proteinSeq'
21 --procodingseq='$genome_annotation.proCodingSeq'
22 --ids='$genome_annotation.ids'
23 #if str($genome_annotation.dbsnpInCoding) != 'None':
24 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
25 #end if
26 #if str($genome_annotation.cosmic) != 'None':
27 --cosmic='$genome_annotation.cosmic"
28 #end if
29 #else:
30 #set index_path = $genome_annotation.builtin.fields.path
31 --exon_anno='$index_path/exon_anno.RData'
32 --proteinseq='$index_path/proseq.RData'
33 --procodingseq='$index_path/procodingseq.RData'
34 --ids='$index_path/ids.RData'
35 #if $genome_annotation.dbsnpInCoding:
36 --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
37 #end if
38 #if $genome_annotation.cosmic:
39 --cosmic='$index_path/cosmic.RData'
40 #end if
41 #end if
42 2>1
43 ]]>
44 </command>
45 <inputs>
46 <conditional name="genome_annotation">
47 <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">
48 <option value="builtin">Use a built-in genome annotation</option>
49 <option value="history">Use annotation from your history</option>
50 </param>
51 <when value="builtin">
52 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
53 <options from_data_table="customProDB">
54 <filter type="sort_by" column="2"/>
55 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
56 </options>
57 </param>
58 <param name="bamInput" type="data" format="bam" label="BAM file">
59 <validator type="unspecified_build" />
60 <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" />
61 </param>
62 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
63 <validator type="unspecified_build" />
64 <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" />
65 </param>-->
66 <param name="vcfInput" type="data" format="vcf" label="VCF file">
67 <validator type="unspecified_build" />
68 <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" />
69 </param>
70 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
71 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
72 </when>
73 <when value="history">
74 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
75 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
76 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
77 <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
78 <param name="bamInput" type="data" format="bam" label="BAM file">
79 <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" />
80 </param>
81 <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
82 <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" />
83 </param>-->
84 <param name="vcfInput" type="data" format="vcf" label="VCF file" />
85 <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
86 <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
87 </when>
88 </conditional>
89 <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." />
90 </inputs>
91 <outputs>
92 <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
93 <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
94 <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
95 </outputs>
96 <tests>
97 <test>
98 <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
99 <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
100 <param name="source" value="history" />
101 <param name="exonAnno" value="exon_anno.RData" />
102 <param name="proteinSeq" value="proseq.RData" />
103 <param name="proCodingSeq" value="procodingseq.RData" />
104 <param name="ids" value="ids.RData" />
105 <output name="output_rpkm" file="test_rpkm.fasta" />
106 <output name="output_snv" file="test_snv.fasta" />
107 <output name="output_indel" file="test_indel.fasta" />
108 </test>
109 </tests>
110 <help>
111 **Description**
112
113 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
114 <citations>
115 <citation type="doi">10.1093/bioinformatics/btt543</citation>
116 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub
117 repository},
118 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
119 {$sha1$}" -->
120 </citations>
121 </tool>