Mercurial > repos > rnateam > blockbuster
diff blockbuster.xml @ 3:7c7ff7a3503f draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit e11f6de08dca72259d2286c442c5464b1f2236d6
| author | rnateam |
|---|---|
| date | Sun, 17 Jan 2016 06:56:03 -0500 |
| parents | 0f3d3f9f120f |
| children |
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--- a/blockbuster.xml Fri Jan 15 07:52:56 2016 -0500 +++ b/blockbuster.xml Sun Jan 17 06:56:03 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="blockbuster" name="blockbuster" version="0.1.1.1"> +<tool id="blockbuster" name="blockbuster" version="0.1.2"> <description>detects blocks of overlapping reads using a gaussian-distribution approach</description> <requirements> <requirement type="package" version="0.0.1.1">blockbuster</requirement> @@ -12,15 +12,20 @@ -scale $scale -merge $merge -tagFilter $tagFilter - -print $print + #if str($print).endswith( 'blocks' ) + -print 1 + #else + -print 2 + #end if $input > data.blockbuster; - #if str($print)=="1" - awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster - #else if str($print)=="2" - awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster + #if str($print) == 'bed_blocks' + awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster > $output + #else if str($print) == 'bed_reads' + awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster > $output + #else + mv data.blockbuster $output #end if - > $output ]]> </command> <inputs> @@ -32,14 +37,33 @@ <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/> <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/> <param name="print" type="select" label="Type of output" > - <option value="1">blocks</option> - <option value="2" selected="True">reads</option> + <option value="bbf_blocks">blocks (blockbuster format)</option> + <option value="bbf_reads" selected="True">reads (blockbuster format)</option> + <option value="bed_blocks">blocks (bed format)</option> + <option value="bed_reads" >reads (bed format)</option> </param> </inputs> <outputs> - <data format="bed" name="output" label="blockbuster on ${on_string}"/> + <data format="bed" name="output" label="blockbuster on ${on_string}"> + <change_format> + <when input="print" value="bbf_blocks" format="tabular" /> + <when input="print" value="bbf_reads" format="tabular" /> + </change_format> + </data> </outputs> + <tests> + <test> + <param name="input" value="blockbuster_test_input.bed" ftype="bed" /> + <param name="print" value="bed_blocks" /> + <output name="output" file="blockbuster_test_result1.bed" ftype="bed" /> + </test> + <test> + <param name="input" value="blockbuster_test_input.bed" ftype="bed" /> + <param name="print" value="bbf_blocks" /> + <output name="output" file="blockbuster_test_result2.blockbuster" ftype="tabular" /> + </test> + </tests> <help> <![CDATA[