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Add missed dbkey setting to Tophat color-space wrapper

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This commit is contained in:
Kelly Vincent
2011-06-27 11:20:04 -04:00
parent 20f77b2a71
commit b2b107724b
2 changed files with 73 additions and 3 deletions
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tools/ngs_rna/tophat_color_wrapper.xml
+72 -2
View File
@@ -391,6 +391,23 @@
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
<filter>
@@ -401,9 +418,62 @@
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/>
</outputs>
<tests>
<!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters -->
tools/ngs_rna/tophat_wrapper.xml
+1 -1
View File
@@ -386,7 +386,7 @@
( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or
( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">