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fix for https://github.com/galaxyproject/tools-iuc/issues/148 #161

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merged 1 commit into from
May 25, 2015
Merged

fix for https://github.com/galaxyproject/tools-iuc/issues/148 #161

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6 changes: 1 addition & 5 deletions tools/bedtools/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -89,10 +89,6 @@
</param>
</xml>

<xml name="choose_column">
<param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
</xml>

<token name="@C_AND_O_ARGUMENT@">
#set $col = list()
#set $op = list()
Expand All @@ -108,7 +104,7 @@

<xml name="c_and_o_argument">
<repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
<expand macro="choose_column" />
<yield />
<expand macro="choose_operations">
<expand macro="math_options" />
<expand macro="additional_math_options" />
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4 changes: 3 additions & 1 deletion tools/bedtools/mapBed.xml
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Expand Up @@ -30,7 +30,9 @@
label="Require reciprocal overlap"
help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
<expand macro="strand2" />
<expand macro="c_and_o_argument" />
<expand macro="c_and_o_argument">
<param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
</expand>
<expand macro="split" />
<expand macro="print_header" />
<conditional name="genome">
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4 changes: 3 additions & 1 deletion tools/bedtools/mergeBed.xml
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Expand Up @@ -28,7 +28,9 @@
label="Maximum distance between features allowed for features to be merged"
help="That is, overlapping and/or book-ended features are merged. (-d)"/>
<expand macro="print_header" />
<expand macro="c_and_o_argument" />
<expand macro="c_and_o_argument">
<param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
</expand>
</inputs>
<outputs>
<data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
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