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Change order of Bowtie2 output datasets to put aligned reads at top of history.

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This commit is contained in:
Jeremy Goecks
2013-01-30 12:55:49 -05:00
parent d0768bac8b
commit 7538091308
1 changed files with 16 additions and 16 deletions
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tools/sr_mapping/bowtie2_wrapper.xml
+16 -16
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@@ -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>