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Modified Tophat wrapper so dbkey will be properly set both for built-in and history references

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This commit is contained in:
Kelly Vincent
2011-05-17 12:05:07 -04:00
parent 2b7025f11d
commit 778088bba9
1 changed files with 74 additions and 4 deletions
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tools/ngs_rna/tophat_wrapper.xml
+74 -4
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@@ -1,4 +1,4 @@
<tool id="tophat" name="Tophat" version="1.2.0">
<tool id="tophat" name="Tophat" version="1.2.1">
<description>Find splice junctions using RNA-seq data</description>
<requirements>
<requirement type="package">tophat</requirement>
@@ -100,7 +100,7 @@
--seg-length=$singlePaired.pParams.seg_length
--library-type=$singlePaired.pParams.library_type
## Indel search.
## Indel search.
#if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
--allow-indels
--max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
@@ -386,6 +386,23 @@
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
<filter>
@@ -396,9 +413,62 @@
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
)
</filter>
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
<action type="metadata" name="dbkey">
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
</option>
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/>
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/>
</outputs>
<tests>