Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.xml @ 0:d01419542f62 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 14 Jan 2016 13:00:56 -0500
parents
children 0d9ce24ea038
comparison
equal deleted inserted replaced
-1:000000000000 0:d01419542f62
1 <tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
2 <description>Generate protein FASTAs from exosome/transcriptome data</description>
3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 </stdio>
6 <command interpreter="Rscript --vanilla">PSM2SAM.R
7 #if str($input).strip() != "":
8 --passedPSM="$input"
9 #end if
10 #if str($scoreColumn).strip() != "":
11 --XScolumn="$scoreColumn"
12 #end if
13 #if str($optionalUserInput.exonAnno).strip() != "None":
14 --exon_anno="$optionalUserInput.exonAnno"
15 #end if
16 #if str($optionalUserInput.proteinSeq).strip() != "None":
17 --proteinseq="$optionalUserInput.proteinSeq"
18 #end if
19 #if str($optionalUserInput.proCodingSeq).strip() != "None":
20 --procodingseq="$optionalUserInput.proCodingSeq"
21 #end if
22 #if str($optionalUserInput.header).strip() != "None":
23 --header="$optionalUserInput.header"
24 #end if
25 #if str($output).strip() != "":
26 --OutputFile="$output"
27 #end if
28
29 2&gt;&amp;1</command>
30 <inputs>
31 <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input PSMs">
32 <validator type="empty_field" message="This field is required."/>
33 </param>
34 <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
35 <validator type="empty_field" message="This field is required."/>
36 </param>
37 <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
38 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
39 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
40 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
41 <param name="header" type="data" format="txt" help="A text file of SAM headers to include in the output file, usually corresponding to the exon and coding sequences used." label="SAM Headers" optional="true" />
42 </section>
43 </inputs>
44 <outputs>
45 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
46 </outputs>
47 <!--<tests>
48 <test>
49 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
50 <param name="scoreColumn" value="Myrimatch:MVH" />
51 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
52 </test>
53 <test>
54 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
55 <param name="scoreColumn" value="Myrimatch:MVH" />
56 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
57 </test>
58 </tests>-->
59 <help>
60 **Description**
61
62 Generate protein FASTAs from exosome/transcriptome data (in the form of BAM files).
63 </help>
64 </tool>