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Changeset 37:497da23fee84 (2018-07-01)

Previous changeset 36:4e47e1caf21a (2018-06-28) Next changeset 38:216a55a39b52 (2018-07-01)

Commit message:
Uploaded

modified:
flexbar.xml

diff -r 4e47e1caf21a -r 497da23fee84 flexbar.xml
--- a/flexbar.xml Thu Jun 28 09:11:58 2018 -0400
+++ b/flexbar.xml Sun Jul 01 06:45:19 2018 -0400

[

@@ -1,9 +1,9 @@

-
+


-<tool id="flexbar" name="Flexbar" version="3.4.1">
+<tool id="flexbar" name="Flexbar" version="3.4.2">

<description>- flexible barcode and adapter removal</description>

@@ -17,18 +17,28 @@

<![CDATA[

- flexbar
+ #if $reads.mode == "se":
+ ln -s '$reads.rs' '$rsout'_input.'$reads.rs.extension' &&
+ #elif $reads.mode == "pe":
+ ln -s '$reads.r1' '$r1out'_input.'$reads.r1.extension' &&
+ ln -s '$reads.r2' '$r2out'_input.'$reads.r2.extension' &&
+ #else:
+ ln -s '$reads.rc.forward' '$rcout.forward'_input.'$reads.rc.forward.extension' &&
+ ln -s '$reads.rc.reverse' '$rcout.reverse'_input.'$reads.rc.reverse.extension' &&
+ #end if
+
+ '$__tool_directory__/flexbar.pl' flexbar

--threads \${GALAXY_SLOTS:-1}

#if $reads.mode == "se":
- --reads '$reads.rs'
+ --reads '$rsout'_input.'$reads.rs.extension'
#elif $reads.mode == "pe":
- --reads '$reads.r1'
- --reads2 '$reads.r2'
+ --reads '$r1out'_input.'$reads.r1.extension'
+ --reads2 '$r2out'_input.'$reads.r2.extension'
#else:
- --reads '$reads.rc.forward'
- --reads2 '$reads.rc.reverse'
+ --reads '$rcout.forward'_input.'$reads.rc.forward.extension'
+ --reads2 '$rcout.reverse'_input.'$reads.rc.reverse.extension'
#end if

--max-uncalled $maxUncalled
@@ -188,13 +198,13 @@

#if $reads.mode == "se":
- --output-reads '$rsout'
+ --output-reads '$rsout'.'$reads.rs.extension'
#elif $reads.mode == "pe":
- --output-reads '$r1out'
- --output-reads2 '$r2out'
+ --output-reads '$r1out'.'$reads.r1.extension'
+ --output-reads2 '$r2out'.'$reads.r2.extension'
#else:
- --output-reads '$rcout.forward'
- --output-reads2 '$rcout.reverse'
+ --output-reads '$rcout.forward'.'$reads.rc.forward.extension'
+ --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'
#end if

--output-log '$outlog'
@@ -212,14 +222,14 @@
<option value="pc">Paired read collection</option>
</param>
<when value="se">
- <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file"/>
+ <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file"/>
</when>
<when value="pe">
- <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 1"/>
- <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 2"/>
+ <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file 1"/>
+ <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file 2"/>
</when>
<when value="pc">
- <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina" type="data_collection" collection_type="paired" label="Fastq pair collection"/>
+ <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" type="data_collection" collection_type="paired" label="Fastq pair collection"/>
</when>
</conditional>