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Change language and parameter names in GOPS subtract to imply that any interval files can be used as input, not just BED files.

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This commit is contained in:
Jeremy Goecks
2010-06-11 14:20:12 -04:00
parent 7f131e91e6
commit 243700630c
1 changed files with 22 additions and 22 deletions
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tools/new_operations/subtract.xml
+22 -22
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@@ -1,10 +1,10 @@
<tool id="gops_subtract_1" name="Subtract">
<description>the intervals of two queries</description>
<command interpreter="python">gops_subtract.py
#if $inputs.type == "BED":
$inputs.bed_input1 $inputs.bed_input2 $output
-1 ${inputs.bed_input1.metadata.chromCol},${inputs.bed_input1.metadata.startCol},${inputs.bed_input1.metadata.endCol},${inputs.bed_input1.metadata.strandCol}
-2 ${inputs.bed_input2.metadata.chromCol},${inputs.bed_input2.metadata.startCol},${inputs.bed_input2.metadata.endCol},${inputs.bed_input2.metadata.strandCol}
#if $inputs.type == "Interval":
$inputs.interval_input1 $inputs.interval_input2 $output
-1 ${inputs.interval_input1.metadata.chromCol},${inputs.interval_input1.metadata.startCol},${inputs.interval_input1.metadata.endCol},${inputs.interval_input1.metadata.strandCol}
-2 ${inputs.interval_input2.metadata.chromCol},${inputs.interval_input2.metadata.startCol},${inputs.interval_input2.metadata.endCol},${inputs.interval_input2.metadata.strandCol}
#else
$inputs.gff_input1 $inputs.gff_input2 $output
## TODO: can we use metadata like above to set these columns rather than hardcode them?
@@ -17,15 +17,15 @@
<inputs>
<conditional name="inputs">
<param name="type" type="select" label="File Format to Use">
<option value="BED">BED</option>
<option value="Interval">Interval</option>
<option value="GFF">GFF</option>
</param>
<when value="BED">
<param format="interval" name="bed_input2" type="data" help="Second query">
<when value="Interval">
<param format="interval" name="interval_input2" type="data" help="Second query">
<label>Subtract</label>
</param>
<param format="interval" name="bed_input1" type="data" help="First query">
<param format="interval" name="interval_input1" type="data" help="First query">
<label>from</label>
</param>
</when>
@@ -52,8 +52,8 @@
</inputs>
<outputs>
<data format="input" name="output">
#if inputs.type == "BED":
metadata_source="inputs.bed_input1"
#if inputs.type == "Interval":
metadata_source="inputs.interval_input1"
#else:
metadata_source="inputs.gff_input1"
#end if
@@ -62,33 +62,33 @@
<code file="operation_filter.py"/>
<tests>
<test>
<param name="type" value="BED"/>
<param name="bed_input1" value="1.bed" />
<param name="bed_input2" value="2.bed" />
<param name="type" value="Interval"/>
<param name="interval_input1" value="1.bed" />
<param name="interval_input2" value="2.bed" />
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops-subtract.dat" />
</test>
<test>
<param name="type" value="BED"/>
<param name="bed_input1" value="1.bed" />
<param name="bed_input2" value="2_mod.bed" ftype="interval"/>
<param name="type" value="Interval"/>
<param name="interval_input1" value="1.bed" />
<param name="interval_input2" value="2_mod.bed" ftype="interval"/>
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops_subtract_diffCols.dat" />
</test>
<test>
<param name="type" value="BED"/>
<param name="bed_input1" value="gops_subtract_bigint.bed" />
<param name="bed_input2" value="2.bed" />
<param name="type" value="Interval"/>
<param name="interval_input1" value="gops_subtract_bigint.bed" />
<param name="interval_input2" value="2.bed" />
<param name="min" value="1" />
<param name="returntype" value="" />
<output name="output" file="gops-subtract.dat" />
</test>
<test>
<param name="type" value="BED"/>
<param name="bed_input1" value="1.bed" />
<param name="bed_input2" value="2.bed" />
<param name="type" value="Interval"/>
<param name="interval_input1" value="1.bed" />
<param name="interval_input2" value="2.bed" />
<param name="min" value="10" />
<param name="returntype" value="Non-overlapping pieces of intervals" />
<output name="output" file="gops-subtract-p.dat" />