Mercurial > repos > iuc > bedtools
changeset 3:2cd7e321d259 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 27 May 2015 12:54:35 -0400 |
| parents | 457b09031d57 |
| children | 607c0576c6ab |
| files | macros.xml mapBed.xml mergeBed.xml shuffleBed.xml |
| diffstat | 4 files changed, 11 insertions(+), 10 deletions(-) [+] |
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--- a/macros.xml Tue May 19 07:05:36 2015 -0400 +++ b/macros.xml Wed May 27 12:54:35 2015 -0400 @@ -89,10 +89,6 @@ </param> </xml> - <xml name="choose_column"> - <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" /> - </xml> - <token name="@C_AND_O_ARGUMENT@"> #set $col = list() #set $op = list() @@ -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" />
--- a/mapBed.xml Tue May 19 07:05:36 2015 -0400 +++ b/mapBed.xml Wed May 27 12:54:35 2015 -0400 @@ -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"> @@ -49,7 +51,7 @@ <param name="inputA" value="mapBed1.bed" ftype="bed" /> <param name="inputB" value="mapBed2.bed" ftype="bed" /> <repeat name="c_and_o_argument_repeat"> - <param name="cols" value="5" /> + <param name="col" value="5" /> <param name="operation" value="mean" /> </repeat> <output name="output" file="mapBed_result1.bed" ftype="bed" /> @@ -67,7 +69,7 @@ <param name="inputA" value="mapBed1.bed" ftype="bed" /> <param name="inputB" value="mapBed2.bed" ftype="bed" /> <repeat name="c_and_o_argument_repeat"> - <param name="cols" value="5" /> + <param name="col" value="5" /> <param name="operation" value="collapse" /> </repeat> <param name="strand" value="-S" /> @@ -77,7 +79,7 @@ <param name="inputA" value="mapBed1.bed" ftype="bed" /> <param name="inputB" value="mapBed2.bed" ftype="bed" /> <repeat name="c_and_o_argument_repeat"> - <param name="cols" value="5" /> + <param name="col" value="5" /> <param name="operation" value="collapse" /> </repeat> <param name="strand" value="-s" />
--- a/mergeBed.xml Tue May 19 07:05:36 2015 -0400 +++ b/mergeBed.xml Wed May 27 12:54:35 2015 -0400 @@ -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}"/>
--- a/shuffleBed.xml Tue May 19 07:05:36 2015 -0400 +++ b/shuffleBed.xml Wed May 27 12:54:35 2015 -0400 @@ -42,6 +42,7 @@ <option value="not_be">Coordinates in which features from -i should not be placed?</option> <option value="be">coordinates in which features from -i should be placed?</option> </param> + <when value="no" /> <when value="not_be"> <param name="excl" type="data" format="bed" label="Choose File" /> <expand macro="overlap" />