diff data_manager/customProDB_annotation.xml @ 1:9b4ee836e35b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6

--- a/data_manager/customProDB_annotation.xml	Tue Mar 14 14:11:55 2017 -0400
+++ b/data_manager/customProDB_annotation.xml	Thu Jun 08 10:55:08 2017 -0400
@@ -1,7 +1,25 @@
-<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
+<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="1.16.1.0">
   <description>builder</description>
   <requirements>
-    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
+    <requirement type="package" version="3.3.1">r-base</requirement>
+    <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
+    <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
+    <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
+    <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
+    <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
+    <requirement type="package" version="1.11.1">r-devtools</requirement>
+    <requirement type="package" version="3.98_1.4">r-xml</requirement>
+    <requirement type="package" version="0.10.11">r-rmysql</requirement>
+    <requirement type="package" version="1.0.2">r-testthat</requirement>
+    <requirement type="package" version="0.1.0">r-getoptlong</requirement>
+    <requirement type="package" version="1.1.2">r-stringi</requirement>
+    <requirement type="package" version="1.1.0">r-stringr</requirement>
+    <requirement type="package" version="1.10.0">r-data.table</requirement>
+    <requirement type="package" version="0.4_10">r-sqldf</requirement>
+    <requirement type="package" version="0.6_6">r-gsubfn</requirement>
+    <requirement type="package" version="2.3_47">r-chron</requirement>
+    <requirement type="package" version="0.3_10">r-proto</requirement>
+    <requirement type="package" version="1.8.4">r-plyr</requirement>
   </requirements>
   <stdio>
     <exit_code range=":-1" />
@@ -9,17 +27,43 @@
   </stdio>
   <command><![CDATA[
     Rscript --vanilla '$__tool_directory__/customProDB_annotation.R'
-    --outputFile '${out_file}'
-    --dbkey '${dbkey}'
-    --dbsnp '${dbsnp}'
-    $cosmic
-    --dbkey_description '${ dbkey.get_display_text() }'
-    2>1
+        --outputFile '${out_file}'
+
+        #if str($transcriptome_annotation.source) == 'refseq':
+          --dbkey '${transcriptome_annotation.dbkey}'
+          --dbkey_description '${ transcriptome_annotation.dbkey.get_display_text().strip("\"'") }'
+        #else:
+          --ensembl_dataset '${transcriptome_annotation.ensembl_dataset.fields.dataset}'
+          --ensembl_host '${transcriptome_annotation.ensembl_dataset.fields.host}'
+          --dbkey_description '${transcriptome_annotation.ensembl_dataset.fields.name}'
+        #end if
+
+        --dbsnp '${dbsnp}'
+        $cosmic
+    2>&1
 ]]>
   </command>
   <inputs>
-    <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
-    <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
+    <conditional name="transcriptome_annotation">
+      <param name="source" type="select" label="What source do you want to use for mapping between genes, transcripts, and proteins?" help="RefSeq transcripts are like NM_xxxx, Ensembl transcripts are like ENSTxxxx">
+        <option value="refseq">Annotate transcriptome with RefSeq (from NCBI/UCSC)</option>
+        <option value="ensembl">Annotate transcriptome with Ensembl (from Biomart)</option>
+      </param>
+      <when value="refseq">
+        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" help="e.g. hg38, hg19, mm10, canFam31" />
+      </when>
+      <when value="ensembl">
+        <param type="select" name="ensembl_dataset" value="" label="Ensembl reference genome identifier">
+          <options from_file="ensembl_datasets.loc">
+            <column name="value" index="2" />
+            <column name="dataset" index="0" />
+            <column name="host" index="1" />
+            <validator type="no_options" message="Ensembl dataset list not loaded"/>
+          </options>
+        </param>
+      </when>
+    </conditional>
+    <param type="text" name="dbsnp" value="" label="dbSNP identifier (select organisms only, e.g. human, mouse, cow)" help="e.g. snp142" />
     <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" />
   </inputs>
   <outputs>
@@ -29,8 +73,12 @@
 
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+This data manager creates the transcriptome annotation in the RData format needed by customProDB.
+Two annotation sources are supported: UCSC and Ensembl.
+Note that because UCSC's table browser only provides current gene annotations for a given genome assembly,
+only the Ensembl annotation is entirely reproducible, i.e. running again with the same settings next month will create the same annotation.
 
+Ensembl chromosome names (1,2, ...) are converted to UCSC format (chr1,chr2, ...) to ease integration with other Galaxy tools.
   </help>
   <citations>
   <citation type="doi">10.1093/bioinformatics/btt543</citation>