changeset 40:cdf2ffe2f8be draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430

--- a/sRbowtie.xml	Tue Jul 04 18:28:46 2017 -0400
+++ b/sRbowtie.xml	Mon Jul 10 13:20:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
+<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.3">
     <description>for FASTA small reads</description>
     <requirements>
         <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
@@ -6,9 +6,11 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $refGenomeSource.genomeSource == "history":
-            bowtie-build -f $refGenomeSource.ownFile local_index &&
+            bowtie-build -f $refGenomeSource.ownFile genome &&
+            ln -s -f '$refGenomeSource.ownFile' genome.fa &&
+            #set index_path = 'genome'
         #else:
-            ln -f -s $refGenomeSource.index.fields.path local_index &&
+            #set index_path = $refGenomeSource.index.fields.path
         #end if
         #if $input.extension == "fasta":
             #set format = "-f"
@@ -46,16 +48,16 @@
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output
         #elif $output_format == "sam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
         #end if
         ##### | samtools view -uS
         ]]></command>
     <inputs>
-        <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
+        <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" />
         <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
             <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
             <option value="unique">Match unique mappers on DNA reference index</option>
@@ -181,7 +183,7 @@
 
 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
 
-The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
+The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.
 
 ------
 
@@ -226,13 +228,13 @@
 
 .. class:: warningmark
 
-*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
+*Lists of reads, in fasta or fastq format, clipped from their adapter sequence*
 
 -----
 
 **OUTPUTS**
 
-If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
+If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format, having the following columns::
 
     Column    Description
   --------    --------------------------------------------------------