Mercurial > repos > iuc > bedtools

diff coverageBed.xml @ 26:95a3b2c25bd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:46 -0400
parents 33c3ddea63c5
children a33db97b220c
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line diff
--- a/coverageBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/coverageBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -39,19 +39,19 @@
 ]]>
     </command>
     <inputs>
-        <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
         <conditional name="reduce_or_iterate">
             <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
                 <option value='iterate' selected='true'>One output file per 'input B' file</option>
                 <option value='reduce'>Single output containing results for all 'input B' files</option>
             </param>
             <when value='iterate'>
-                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
             <when value='reduce'>
-                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
         </conditional>
         <expand macro="split" />
@@ -69,14 +69,14 @@
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=",."/></valid>
             </sanitizer>
-	</param>
+        </param>
         <param name="overlap_b" type="text"
             label="Minimum overlap required as a fraction of B."
             help="Default is 1E-9 (i.e., 1bp). (-F)">
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=",."/></valid>
             </sanitizer>
-	</param>
+        </param>
         <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
             label="Require that the fraction overlap be reciprocal for A AND B."
             help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />