Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.xml @ 5:6db27bef602f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 29 Jan 2016 16:03:10 -0500
parents 7e078d4e40f8
children 61e45c111ef7
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1 <tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
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2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Job Failed" />
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5 </stdio>
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6 <command interpreter="Rscript --vanilla">customProDB.R
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8 --bam="$bamInput"
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9 --vcf="$vcfInput"
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10 --outputFile="$output"
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12 #if str($genome_annotation.source) == "history":
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13 --exon_anno="$genome_annotation.exonAnno"
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14 --proteinseq="$genome_annotation.proteinSeq"
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15 --procodingseq="$genome_annotation.proCodingSeq"
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16 #else:
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17 #set index_path = $genome_annotation.builtin.fields.path
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18 --exon_anno="$index_path/exon_anno.RData"
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19 --proteinseq="$index_path/proseq.RData"
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20 --procodingseq="$index_path/procodingseq.RData"
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21 #end if
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23 2&gt;&amp;1</command>
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24 <inputs>
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25 <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
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26 <validator type="empty_field" message="This field is required."/>
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27 </param>
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28 <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
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29 <validator type="empty_field" message="This field is required."/>
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30 </param>
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32 <conditional name="genome_annotation">
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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">
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34 <option value="builtin">Use a built-in genome annotation</option>
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35 <option value="history">Use a genome from the history and build index</option>
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36 </param>
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37 <when value="builtin">
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38 <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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39 <options from_data_table="customProDB">
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40 <filter type="sort_by" column="2"/>
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41 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
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42 </options>
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43 </param>
2
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44 </when>
3
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45 <when value="history">
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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" />
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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" />
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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" />
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
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54 </outputs>
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55 <!--<tests>
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56 <test>
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57 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
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58 <param name="scoreColumn" value="Myrimatch:MVH" />
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59 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
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60 </test>
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61 <test>
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62 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
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63 <param name="scoreColumn" value="Myrimatch:MVH" />
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64 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
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65 </test>
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66 </tests>-->
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67 <help>
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68 **Description**
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69
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70 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
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71 </help>
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72 </tool>