diff customProDB.xml @ 6:61e45c111ef7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 03 Feb 2016 12:37:47 -0500
parents 6db27bef602f
children b83a4002aab1
line wrap: on
line diff
--- a/customProDB.xml	Fri Jan 29 16:03:10 2016 -0500
+++ b/customProDB.xml	Wed Feb 03 12:37:47 2016 -0500
@@ -5,34 +5,30 @@
   </stdio>
   <command interpreter="Rscript --vanilla">customProDB.R
 
-       --bam="$bamInput"
-       --vcf="$vcfInput"
-       --outputFile="$output"
+       --bam="$genome_annotation.bamInput"
+       --bai="${genome_annotation.bamInput.metadata.bam_index}"
+       --vcf="$genome_annotation.vcfInput"
+       --outputFile="${output_rpkm}"
 
        #if str($genome_annotation.source) == "history":
             --exon_anno="$genome_annotation.exonAnno"
             --proteinseq="$genome_annotation.proteinSeq"
             --procodingseq="$genome_annotation.proCodingSeq"
+            --ids="$genome_annotation.ids"
        #else:
             #set index_path = $genome_annotation.builtin.fields.path
             --exon_anno="$index_path/exon_anno.RData"
             --proteinseq="$index_path/proseq.RData"
             --procodingseq="$index_path/procodingseq.RData"
+            --ids="$index_path/ids.RData"
        #end if
 
 2&gt;&amp;1</command>
   <inputs>
-    <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
-      <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>
-
     <conditional name="genome_annotation">
       <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">
         <option value="builtin">Use a built-in genome annotation</option>
-        <option value="history">Use a genome from the history and build index</option>
+        <option value="history">Use annotation from your history</option>
       </param>
       <when value="builtin">
         <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
@@ -41,29 +37,53 @@
             <validator type="no_options" message="No annotations are available for the selected input dataset"/>
           </options>
         </param>
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <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" />
+        </param>
+        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
+            <validator type="unspecified_build" />
+            <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" />
+        </param>-->
+        <param name="vcfInput" type="data" format="vcf" label="VCF file">
+            <validator type="unspecified_build" />
+            <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" />
+        </param>
       </when>
       <when value="history">
-        <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" />
-        <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" />
-        <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" />
+        <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
+        <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" />
+        <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" />
+        <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <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" />
+        </param>
+        <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
+            <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" />
+        </param>
+        <param name="vcfInput" type="data" format="vcf" label="VCF file" />
       </when>
     </conditional>
   </inputs>
   <outputs>
-    <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
+    <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
+    <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
+    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
   </outputs>
-  <!--<tests>
+  <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" />
+      <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
+      <param name="source" value="history" />
+      <param name="exonAnno" value="exon_anno.RData" />
+      <param name="proteinSeq" value="proseq.RData" />
+      <param name="proCodingSeq" value="procodingseq.RData" />
+      <param name="ids" value="ids.RData" />
+      <output name="output_rpkm" file="test_rpkm.fasta" />
+      <output name="output_snv" file="test_snv.fasta" />
+      <output name="output_indel" file="test_indel.fasta" />
     </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>-->
+  </tests>
   <help>
 **Description**