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Update bowtie tool output dataset actions to reference columns in the new location file style.

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FIXME: Tool output actions need to be made data_table aware.
This commit is contained in:
Daniel Blankenberg
2010-11-22 16:02:43 -05:00
parent 07ee21b4cb
commit e42b3e1b01
2 changed files with 4 additions and 20 deletions
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tools/sr_mapping/bowtie_color_wrapper.xml
+2 -10
View File
@@ -317,21 +317,13 @@
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_file" name="bowtie_indices_color.loc" column="0" offset="0">
<option type="from_file" name="bowtie_indices_color.loc" column="1" offset="0">
<filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="1"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
</conditional>
<!-- Special casing equCab2chrM to equCab2 -->
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
<filter type="insert_column" column="0" value="equCab2chrM"/>
<filter type="insert_column" column="0" value="equCab2"/>
<filter type="metadata_value" ref="output" name="dbkey" column="1" />
</option>
</action>
</actions>
</data>
</outputs>
tools/sr_mapping/bowtie_wrapper.xml
+2 -10
View File
@@ -300,21 +300,13 @@
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_file" name="bowtie_indices.loc" column="0" offset="0">
<option type="from_file" name="bowtie_indices.loc" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="1"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
</conditional>
<!-- Special casing equCab2chrM to equCab2 -->
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
<filter type="insert_column" column="0" value="equCab2chrM"/>
<filter type="insert_column" column="0" value="equCab2"/>
<filter type="metadata_value" ref="output" name="dbkey" column="1" />
</option>
</action>
</actions>
</data>
</outputs>