1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/95e33df0ae03/ changeset: 95e33df0ae03 user: jgoecks date: 2013-01-30 18:55:49 summary: Change order of Bowtie2 output datasets to put aligned reads at top of history. affected #: 1 file

diff -r 6a03e7197bdc83512444d66bfd793e0c91596217 -r 95e33df0ae0332e04f14646abbf77c02672ef23a tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -145,6 +145,22 @@ </inputs><outputs> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data><data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"> @@ -164,22 +180,6 @@ </conditional></actions></data> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > - <filter>unalignedFile is True</filter> - <actions> - <action type="format"> - <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> - </action> - </actions> - </data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> - <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> - <actions> - <action type="format"> - <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> - </action> - </actions> - </data></outputs><tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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