Mercurial > repos > rnateam > blockbuster
changeset 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 | |
| files | blockbuster.xml test-data/blockbuster_test_input.bed test-data/blockbuster_test_result1.bed test-data/blockbuster_test_result2.blockbuster |
| diffstat | 4 files changed, 142 insertions(+), 10 deletions(-) [+] |
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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[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blockbuster_test_input.bed Sun Jan 17 06:56:03 2016 -0500 @@ -0,0 +1,100 @@ +chr1 4264 4284 GSM450600_692367 0.166666666666667 - +chr1 7272 7293 GSM450600_221042 0.333333333333333 - +chr1 7273 7294 GSM450600_549504 0.166666666666667 - +chr1 13755 13775 GSM450600_440425 0.2 - +chr1 23387 23420 GSM450600_770553 0.142857142857143 - +chr1 76462 76483 GSM450600_947688 0.333333333333333 - +chr1 84585 84608 GSM450600_960767 0.0769230769230769 - +chr1 99112 99134 GSM450600_1351025 0.142857142857143 - +chr1 101231 101261 GSM450600_1031113 0.2 - +chr1 122477 122501 GSM450600_797617 0.166666666666667 - +chr1 124544 124567 GSM450600_379210 0.0434782608695652 - +chr1 130303 130322 GSM450600_400545 0.0208333333333333 - +chr1 134202 134223 GSM450600_1353082 0.0181818181818182 - +chr1 136192 136210 GSM450600_1354597 0.0714285714285714 - +chr1 137861 137880 GSM450600_33797 0.0416666666666667 - +chr1 234779 234799 GSM450600_865810 0.142857142857143 - +chr1 245433 245455 GSM450600_1351025 0.142857142857143 - +chr1 247546 247576 GSM450600_1031113 0.2 - +chr1 311539 311562 GSM450600_391053 0.0714285714285714 - +chr1 321904 321926 GSM450600_252343 0.1 - +chr1 324192 324211 GSM450600_406528 0.0588235294117647 - +chr1 326847 326867 GSM450600_1295545 0.0454545454545455 - +chr1 330252 330273 GSM450600_451299 0.25 - +chr1 331780 331806 GSM450600_524135 0.00636942675159236 - +chr1 369341 369363 GSM450600_1277722 0.25 - +chr1 529311 529331 GSM450600_1007465 0.2 - +chr1 541704 541736 GSM450600_555018 0.142857142857143 - +chr1 543701 543723 GSM450600_194993 1 - +chr1 554367 554391 GSM450600_539207 1 - +chr1 554558 554578 GSM450600_666162 1 - +chr1 554632 554652 GSM450600_573049 1 - +chr1 554745 554764 GSM450600_646265 1 - +chr1 554746 554770 GSM450600_361920 2 - +chr1 554749 554770 GSM450600_361919 2 - +chr1 554750 554770 GSM450600_361923 0.5 - +chr1 554751 554769 GSM450600_631513 1 - +chr1 554751 554770 GSM450600_361918 3 - +chr1 554751 554771 GSM450600_449223 2 - +chr1 554751 554772 GSM450600_858537 1 - +chr1 554751 554772 GSM450600_860793 3 - +chr1 554752 554770 GSM450600_361917 3 - +chr1 554752 554771 GSM450600_449222 1 - +chr1 554752 554772 GSM450600_860792 1 - +chr1 554753 554771 GSM450600_449221 2 - +chr1 554753 554772 GSM450600_860791 1 - +chr1 554753 554773 GSM450600_518465 2 - +chr1 554753 554774 GSM450600_902806 2 - +chr1 554754 554772 GSM450600_860790 1 - +chr1 554754 554774 GSM450600_902805 1 - +chr1 554754 554775 GSM450600_1395213 0.333333333333333 - +chr1 554757 554779 GSM450600_1270609 0.333333333333333 - +chr1 554760 554778 GSM450600_618071 0.333333333333333 - +chr1 554760 554781 GSM450600_1407453 0.333333333333333 - +chr1 554761 554781 GSM450600_1407452 0.333333333333333 - +chr1 554769 554792 GSM450600_578456 0.2 - +chr1 554772 554794 GSM450600_1272454 0.333333333333333 - +chr1 554772 554794 GSM450600_1272458 0.666666666666667 - +chr1 554772 554795 GSM450600_677346 0.333333333333333 - +chr1 554773 554794 GSM450600_1272457 1.33333333333333 - +chr1 554773 554794 GSM450600_501767 0.666666666666667 - +chr1 554773 554795 GSM450600_677345 0.333333333333333 - +chr1 554773 554797 GSM450600_371690 0.5 - +chr1 554773 554797 GSM450600_371692 0.333333333333333 - +chr1 554774 554794 GSM450600_1272456 0.333333333333333 - +chr1 554775 554797 GSM450600_371689 0.5 - +chr1 554776 554796 GSM450600_649963 0.5 - +chr1 554776 554797 GSM450600_371685 0.5 - +chr1 554776 554797 GSM450600_371686 0.5 - +chr1 554776 554797 GSM450600_371688 0.5 - +chr1 554776 554798 GSM450600_804555 1 - +chr1 554776 554798 GSM450600_804556 1 - +chr1 554776 554802 GSM450600_675133 2 - +chr1 554776 554813 GSM450600_795292 1 - +chr1 554776 554813 GSM450600_795335 1 - +chr1 554777 554797 GSM450600_371691 1 - +chr1 554777 554813 GSM450600_795290 1 - +chr1 554778 554796 GSM450600_649962 0.5 - +chr1 554778 554797 GSM450600_371684 1.5 - +chr1 554778 554797 GSM450600_371687 1 - +chr1 554778 554798 GSM450600_804553 10 - +chr1 554778 554798 GSM450600_804554 1 - +chr1 554778 554798 GSM450600_804557 1 - +chr1 554778 554799 GSM450600_387204 4 - +chr1 554778 554800 GSM450600_571277 11 - +chr1 554778 554800 GSM450600_571278 4 - +chr1 554778 554800 GSM450600_571281 1 - +chr1 554778 554800 GSM450600_571282 1 - +chr1 554778 554801 GSM450600_1168796 0.5 - +chr1 554778 554801 GSM450600_1168956 1 - +chr1 554778 554802 GSM450600_675134 1 - +chr1 554778 554813 GSM450600_795150 1 - +chr1 554778 554813 GSM450600_795289 1 - +chr1 554778 554813 GSM450600_795291 1 - +chr1 554778 554813 GSM450600_795343 1 - +chr1 554779 554797 GSM450600_371682 46 - +chr1 554779 554798 GSM450600_804552 67 - +chr1 554779 554799 GSM450600_248038 0.5 - +chr1 554779 554799 GSM450600_387203 29 - +chr1 554779 554799 GSM450600_387207 2 - +chr1 554779 554800 GSM450600_571276 11 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blockbuster_test_result1.bed Sun Jan 17 06:56:03 2016 -0500 @@ -0,0 +1,4 @@ +chr1 554745 554813 >cluster_1 243.50 - 554745 554813 +chr1 554772 554813 block_1 213.33 - 554772 554813 +chr1 554746 554779 block_2 29.17 - 554746 554779 +chr1 554745 554764 block_3 1.00 - 554745 554764