Mercurial > repos > crs4 > edge_pro
changeset 4:d5464c9e1723 draft
Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
author | crs4 |
---|---|
date | Tue, 17 Mar 2015 10:44:33 -0400 |
parents | ddcbf8732706 |
children | 407b894abb08 |
files | edge_pro.xml readme.rst |
diffstat | 2 files changed, 18 insertions(+), 4 deletions(-) [+] |
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--- a/edge_pro.xml Mon Jan 19 12:48:51 2015 -0500 +++ b/edge_pro.xml Tue Mar 17 10:44:33 2015 -0400 @@ -10,11 +10,18 @@ -g $genome -p $ptt -r $rnt - ## First input file always required - -u $singlePaired.input1 - ## Second input only if input is paired-end - #if $singlePaired.sPaired == "paired" + + #if $singlePaired.sPaired == "single" + -u $singlePaired.input1 + #else if $singlePaired.sPaired == "paired" + -u $singlePaired.input1 -v $singlePaired.input2 + #else if $singlePaired.sPaired == "pairedCollection" + -u $singlePaired.input.forward + -v $singlePaired.input.reverse + #end if + + #if $singlePaired.sPaired in ["paired", "pairedCollection"] #if str($singlePaired.minInsertSize) -m $singlePaired.minInsertSize #end if @@ -52,6 +59,7 @@ <param name="sPaired" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> + <option value="pairedCollection">Paired-end collection</option> </param> <when value="single"> <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/> @@ -62,6 +70,11 @@ <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" /> <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" /> </when> + <when value="pairedCollection"> + <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> + <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" /> + <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" /> + </when> </conditional> <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" />
--- a/readme.rst Mon Jan 19 12:48:51 2015 -0500 +++ b/readme.rst Tue Mar 17 10:44:33 2015 -0400 @@ -26,6 +26,7 @@ Version history --------------- +- Release 4: Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes). - Release 3: Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation. - Release 2: Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation. - Release 1: Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .