changeset 0:d01419542f62 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/customProDB.xml	Thu Jan 14 13:00:56 2016 -0500
@@ -0,0 +1,64 @@
+<tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
+  <description>Generate protein FASTAs from exosome/transcriptome data</description>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+  </stdio>
+  <command interpreter="Rscript --vanilla">PSM2SAM.R
+       #if str($input).strip() != "":
+          --passedPSM="$input"
+       #end if
+       #if str($scoreColumn).strip() != "":
+          --XScolumn="$scoreColumn"
+       #end if
+       #if str($optionalUserInput.exonAnno).strip() != "None":
+          --exon_anno="$optionalUserInput.exonAnno"
+       #end if
+       #if str($optionalUserInput.proteinSeq).strip() != "None":
+          --proteinseq="$optionalUserInput.proteinSeq"
+       #end if
+       #if str($optionalUserInput.proCodingSeq).strip() != "None":
+          --procodingseq="$optionalUserInput.proCodingSeq"
+       #end if
+       #if str($optionalUserInput.header).strip() != "None":
+          --header="$optionalUserInput.header"
+       #end if
+       #if str($output).strip() != "":
+          --OutputFile="$output"
+       #end if
+
+2&gt;&amp;1</command>
+  <inputs>
+    <param name="input" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input PSMs">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
+      <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
+      <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" />
+      <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" />
+      <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" />
+    </section>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
+  </outputs>
+  <!--<tests>
+    <test>
+      <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
+      <param name="scoreColumn" value="Myrimatch:MVH" />
+      <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
+    </test>
+    <test>
+      <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
+      <param name="scoreColumn" value="Myrimatch:MVH" />
+      <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
+    </test>
+  </tests>-->
+  <help>
+**Description**
+
+Generate protein FASTAs from exosome/transcriptome data (in the form of BAM files).
+</help>
+</tool>
\ No newline at end of file