Mercurial > repos > iuc > bedtools
diff closestBed.xml @ 47:2892111d91f8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
| author | iuc |
|---|---|
| date | Fri, 21 Feb 2025 21:40:09 +0000 |
| parents | 07e8b80f278c |
| children |
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--- a/closestBed.xml Sat May 18 23:28:38 2024 +0000 +++ b/closestBed.xml Fri Feb 21 21:40:09 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>find the closest, potentially non-overlapping interval</description> <macros> <import>macros.xml</import> @@ -14,6 +14,8 @@ -D $addition2.addition2_select $addition2.iu $addition2.id + $addition2.fu + $addition2.fd #end if $io -mdb $mdb @@ -109,50 +111,50 @@ <tests> <test> <param name="inputA" value="closestBedA.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBedB.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBedB.bed" ftype="bed" /> <output name="output" file="closestBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_a.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> <param name="addition" value="true" /> <output name="output" file="closestBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_a.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> <param name="addition" value="True" /> <param name="mdb" value="all" /> <output name="output" file="closestBed_result3.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_c.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_d.bed" ftype="bed" /> - <param name="addition2_select" value="ref" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" /> + <param name="addition2|addition2_select" value="ref" /> <output name="output" file="closestBed_result4.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_c.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_d.bed" ftype="bed" /> - <param name="addition2_select" value="a" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" /> + <param name="addition2|addition2_select" value="a" /> <output name="output" file="closestBed_result5.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBedA.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="a.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="a.bed" ftype="bed" /> <param name="k" value="3" /> <output name="output" file="closestBed_result6.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBedA.bed" ftype="bed" /> - <param name="source" value="data_table" /> - <param name="inputB" value="testid" /> + <param name="overlap_with|source" value="data_table" /> + <param name="overlap_with|table" value="testid" /> <param name="k" value="3" /> <output name="output" file="closestBed_result6.bed" ftype="bed" /> </test>