Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.xml @ 0:d01419542f62 draft

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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
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d01419542f62 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
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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/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">PSM2SAM.R
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7 #if str($input).strip() != "":
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8 --passedPSM="$input"
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9 #end if
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10 #if str($scoreColumn).strip() != "":
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11 --XScolumn="$scoreColumn"
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12 #end if
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13 #if str($optionalUserInput.exonAnno).strip() != "None":
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14 --exon_anno="$optionalUserInput.exonAnno"
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15 #end if
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16 #if str($optionalUserInput.proteinSeq).strip() != "None":
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17 --proteinseq="$optionalUserInput.proteinSeq"
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18 #end if
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19 #if str($optionalUserInput.proCodingSeq).strip() != "None":
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20 --procodingseq="$optionalUserInput.proCodingSeq"
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21 #end if
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22 #if str($optionalUserInput.header).strip() != "None":
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23 --header="$optionalUserInput.header"
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24 #end if
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25 #if str($output).strip() != "":
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26 --OutputFile="$output"
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27 #end if
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28
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29 2&gt;&amp;1</command>
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30 <inputs>
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31 <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input PSMs">
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32 <validator type="empty_field" message="This field is required."/>
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33 </param>
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34 <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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35 <validator type="empty_field" message="This field is required."/>
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36 </param>
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37 <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
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38 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
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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" />
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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" />
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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" />
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42 </section>
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43 </inputs>
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44 <outputs>
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45 <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
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46 </outputs>
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47 <!--<tests>
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48 <test>
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49 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
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50 <param name="scoreColumn" value="Myrimatch:MVH" />
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51 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
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52 </test>
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53 <test>
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54 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
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55 <param name="scoreColumn" value="Myrimatch:MVH" />
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56 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
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57 </test>
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58 </tests>-->
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59 <help>
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60 **Description**
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61
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62 Generate protein FASTAs from exosome/transcriptome data (in the form of BAM files).
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63 </help>
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64 </tool>