| Next changeset 1:605bb64c2668 (2018-04-18) |
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Commit message:
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko commit bd6737d0fba64ed6e7d3be5267868942674696ea |
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added:
miranda2asko.pl miranda2asko.xml test-data/miranda.asko.out test-data/miranda.out |
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| diff -r 000000000000 -r 3f6cdc878f35 miranda2asko.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/miranda2asko.pl Thu Apr 12 10:53:04 2018 -0400 |
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| @@ -0,0 +1,17 @@ +use strict; +use warnings; + +my $miranda=shift; +open MIRANDA, $miranda or die "failed to open $miranda\n"; + +print "mirna\ttargets\@mRNA\tscore\tenergy\talignment length\tglobal coverage\tseed coverage\n"; + +while (<MIRANDA>) { + chomp; + my ($mirna, $target, $score, $energy,$pos1, $pos2,$alnlength, $glcov, $seedcov)=split "\t"; + $mirna=~ s/^>//; + $target=~s/_UTR3$//; + $glcov=~ s/\%$//; + $seedcov=~ s/\%$//; + print join ("\t", $mirna, $target, $score, $energy,$alnlength, $glcov, $seedcov), "\n"; +} |
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| diff -r 000000000000 -r 3f6cdc878f35 miranda2asko.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/miranda2asko.xml Thu Apr 12 10:53:04 2018 -0400 |
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| @@ -0,0 +1,32 @@ +<tool id="miranda2asko" name="Convert miRanda output to tabular" version="0.1"> + <description>for AskOmics</description> + <requirements> + <requirement type="package" version="5.22.2.1">perl</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + perl '$__tool_directory__/miranda2asko.pl' '${miranda}' > '${mirasko}' + ]]></command> + + <inputs> + <param format="tsv" name="miranda" type="data" label="miRanda output" /> + </inputs> + + <outputs> + <data format="tsv" name="mirasko" label="${tool.name} on ${on_string} : AskOmics miRanda output" /> + </outputs> + + <tests> + <test> + <param name="miranda" ftype="tsv" value="miranda.out" /> + <output name="mirasko" ftype="tsv" file="miranda.asko.out" compare="sim_size" /> + </test> + </tests> + + <help> + Generates a TSV compliant to AskOmics from the miRanda output. + </help> + + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 3f6cdc878f35 test-data/miranda.asko.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miranda.asko.out Thu Apr 12 10:53:04 2018 -0400 |
| b |
| b'@@ -0,0 +1,1001 @@\n+mirna\ttargets@mRNA\tscore\tenergy\talignment length\tglobal coverage\tseed coverage\n+api-miR-3015c\trna27318\t146.00\t-13.54\t17\t64.71\t88.24\n+api-miR-3015c\trna14037\t141.00\t-16.27\t16\t68.75\t81.25\n+api-miR-3015c\trna15090\t140.00\t-11.77\t15\t66.67\t86.67\n+api-miR-3015c\trna25490\t145.00\t-12.86\t18\t66.67\t88.89\n+api-miR-3015c\trna23800\t163.00\t-15.96\t18\t72.22\t83.33\n+api-miR-3015c\trna28874\t141.00\t-13.48\t15\t80.00\t86.67\n+api-miR-3015c\trna5471\t145.00\t-17.38\t18\t72.22\t83.33\n+api-miR-3015c\trna16140\t142.00\t-15.04\t17\t64.71\t82.35\n+api-miR-3015c\trna16105\t141.00\t-16.02\t17\t70.59\t88.24\n+api-miR-3015c\trna142\t150.00\t-17.80\t17\t70.59\t88.24\n+api-miR-3015c\trna28003\t146.00\t-11.43\t15\t73.33\t80.00\n+api-miR-3015c\trna6629\t140.00\t-11.26\t17\t70.59\t82.35\n+api-miR-3015c\trna31159\t154.00\t-15.85\t17\t76.47\t88.24\n+api-miR-3015c\trna7103\t154.00\t-14.69\t19\t73.68\t73.68\n+api-miR-3015c\trna27233\t161.00\t-13.68\t16\t81.25\t81.25\n+api-miR-3015c\trna25366\t143.00\t-11.32\t18\t66.67\t77.78\n+api-miR-3015c\trna13454\t144.00\t-11.74\t17\t70.59\t88.24\n+api-miR-3015c\trna16129\t140.00\t-11.44\t7\t100.00\t100.00\n+api-miR-3015c\trna21816\t155.00\t-16.34\t18\t77.78\t83.33\n+api-miR-3015c\trna1484\t150.00\t-13.99\t17\t76.47\t82.35\n+api-miR-3015c\trna9925\t156.00\t-15.91\t17\t82.35\t94.12\n+api-miR-3015c\trna22538\t142.00\t-16.96\t16\t68.75\t87.50\n+api-miR-3015c\trna10626\t143.00\t-11.27\t14\t71.43\t92.86\n+api-miR-3015c\trna8007\t141.00\t-10.21\t16\t68.75\t81.25\n+api-miR-3015c\trna13271\t156.00\t-13.56\t17\t76.47\t82.35\n+api-miR-3015c\trna19614\t150.00\t-15.29\t9\t100.00\t100.00\n+api-miR-3015c\trna7395\t146.00\t-12.72\t17\t64.71\t88.24\n+api-miR-3015c\trna24477\t140.00\t-12.34\t15\t66.67\t86.67\n+api-miR-3015c\trna21283\t169.00\t-16.42\t18\t83.33\t88.89\n+api-miR-3015c\trna18527\t151.00\t-13.33\t17\t70.59\t82.35\n+api-miR-3015c\trna3409\t148.00\t-13.28\t17\t76.47\t88.24\n+api-miR-3015c\trna22964\t143.00\t-13.51\t18\t61.11\t83.33\n+api-miR-3015c\trna15636\t141.00\t-14.21\t18\t66.67\t83.33\n+api-miR-3015c\trna15636\t141.00\t-12.11\t20\t65.00\t80.00\n+api-miR-3015c\trna18504\t151.00\t-13.33\t17\t70.59\t82.35\n+api-miR-3015c\trna8921\t157.00\t-15.36\t12\t91.67\t91.67\n+api-miR-3015c\trna10851\t147.00\t-12.83\t14\t78.57\t92.86\n+api-miR-3015c\trna15581\t147.00\t-11.38\t14\t78.57\t92.86\n+api-miR-3015c\trna11089\t151.00\t-18.87\t16\t81.25\t93.75\n+api-miR-3015c\trna19278\t144.00\t-11.18\t13\t76.92\t84.62\n+api-miR-3015c\trna7087\t157.00\t-13.96\t18\t72.22\t83.33\n+api-miR-3015c\trna23299\t142.00\t-10.62\t17\t76.47\t88.24\n+api-miR-3015c\trna14645\t145.00\t-11.11\t16\t68.75\t87.50\n+api-miR-3015c\trna19270\t140.00\t-15.57\t14\t78.57\t85.71\n+api-miR-3015c\trna69\t148.00\t-14.46\t13\t76.92\t92.31\n+api-miR-3015c\trna3686\t170.00\t-24.54\t17\t88.24\t100.00\n+api-miR-3015c\trna2350\t143.00\t-14.11\t16\t75.00\t87.50\n+api-miR-3015c\trna4825\t146.00\t-9.09\t17\t70.59\t82.35\n+api-miR-3015c\trna4825\t140.00\t-10.23\t7\t100.00\t100.00\n+api-miR-3015c\trna22288\t151.00\t-19.87\t17\t76.47\t88.24\n+api-miR-3015c\trna17118\t157.00\t-16.53\t18\t72.22\t83.33\n+api-miR-3015c\trna18729\t145.00\t-12.23\t16\t68.75\t87.50\n+api-miR-3015c\trna17281\t142.00\t-9.46\t17\t64.71\t82.35\n+api-miR-3015c\trna28869\t142.00\t-14.75\t15\t73.33\t93.33\n+api-miR-3015c\trna17162\t140.00\t-11.21\t19\t73.68\t78.95\n+api-miR-3015c\trna30664\t146.00\t-13.33\t17\t64.71\t88.24\n+api-miR-3015c\trna26576\t161.00\t-15.86\t19\t73.68\t84.21\n+api-miR-3015c\trna26576\t147.00\t-16.61\t16\t81.25\t87.50\n+api-miR-3015c\trna4495\t140.00\t-13.37\t17\t70.59\t82.35\n+api-miR-3015c\trna3554\t143.00\t-25.61\t18\t83.33\t94.44\n+api-miR-3015c\trna664\t168.00\t-18.83\t17\t88.24\t88.24\n+api-miR-3015c\trna5675\t150.00\t-15.84\t18\t72.22\t77.78\n+api-miR-3015c\trna28029\t154.00\t-13.63\t17\t70.59\t94.12\n+api-miR-3015c\trna5749\t140.00\t-13.33\t11\t81.82\t100.00\n+api-miR-3015c\trna6758\t162.00\t-13.43\t17\t76.47\t82.35\n+api-miR-3015c\trna3547\t141.00\t-11.77\t14\t78.57\t92.86\n+api-miR-3015c\trna7883\t146.00\t-16.70\t20\t70.00\t80.00\n+api-miR-3015c\trna11700\t156.00\t-15.85\t17\t70.59\t88.24\n+api-miR-3015c\trna24912\t175.00\t-20.91\t18\t83.33\t88.89\n+api-miR-3015c\trna25062\t140.00\t-11.00\t17\t70.59\t82.35\n+api-miR-3015c\trna26735\t153.00\t-18.27\t18\t72.22\t94.44\n+api-miR-3015c\trna21064\t157.00\t-16.73\t19\t68.42\t84.21\n+api-miR-3015c\trna21064\t146.00\t-17.62\t9\t88.89\t100.00\n+api-miR-3015c\trna10220\t140.00\t-13.36\t18\t72.22\t77.78\n+ap'..b'0.00\n+api-miR-279a\trna18404\t140.00\t-14.45\t7\t100.00\t100.00\n+api-miR-279a\trna8084\t157.00\t-15.05\t18\t77.78\t77.78\n+api-miR-279a\trna8084\t142.00\t-11.00\t15\t73.33\t73.33\n+api-miR-279a\trna2256\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna27026\t150.00\t-13.26\t21\t66.67\t71.43\n+api-miR-279a\trna28583\t140.00\t-9.26\t7\t100.00\t100.00\n+api-miR-279a\trna14556\t145.00\t-10.53\t8\t100.00\t100.00\n+api-miR-279a\trna5401\t140.00\t-7.96\t7\t100.00\t100.00\n+api-miR-279a\trna8818\t141.00\t-10.25\t8\t87.50\t100.00\n+api-miR-279a\trna27253\t141.00\t-19.11\t20\t70.00\t80.00\n+api-miR-279a\trna26199\t143.00\t-9.96\t17\t70.59\t70.59\n+api-miR-279a\trna6208\t140.00\t-8.43\t7\t100.00\t100.00\n+api-miR-279a\trna12634\t140.00\t-10.64\t7\t100.00\t100.00\n+api-miR-279a\trna2213\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna4278\t151.00\t-17.35\t12\t91.67\t91.67\n+api-miR-279a\trna16360\t140.00\t-8.46\t7\t100.00\t100.00\n+api-miR-279a\trna3294\t145.00\t-13.99\t8\t100.00\t100.00\n+api-miR-279a\trna21213\t147.00\t-21.46\t16\t81.25\t87.50\n+api-miR-279a\trna2565\t145.00\t-12.32\t8\t100.00\t100.00\n+api-miR-279a\trna13819\t160.00\t-19.91\t17\t82.35\t82.35\n+api-miR-279a\trna14390\t150.00\t-24.63\t15\t86.67\t93.33\n+api-miR-279a\trna27924\t149.00\t-16.21\t14\t78.57\t85.71\n+api-miR-279a\trna16359\t140.00\t-8.46\t7\t100.00\t100.00\n+api-miR-279a\trna22198\t140.00\t-11.69\t7\t100.00\t100.00\n+api-miR-279a\trna7992\t150.00\t-18.65\t15\t80.00\t80.00\n+api-miR-279a\trna24977\t145.00\t-11.63\t8\t100.00\t100.00\n+api-miR-279a\trna16281\t145.00\t-12.65\t8\t100.00\t100.00\n+api-miR-279a\trna17858\t140.00\t-11.47\t7\t100.00\t100.00\n+api-miR-279a\trna25009\t147.00\t-14.16\t16\t75.00\t75.00\n+api-miR-279a\trna2214\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna15732\t140.00\t-8.46\t7\t100.00\t100.00\n+api-miR-279a\trna27885\t141.00\t-12.34\t8\t87.50\t100.00\n+api-miR-279a\trna5465\t142.00\t-9.54\t15\t73.33\t73.33\n+api-miR-279a\trna15011\t145.00\t-9.77\t8\t100.00\t100.00\n+api-miR-279a\trna13817\t160.00\t-19.91\t17\t82.35\t82.35\n+api-miR-279a\trna15352\t145.00\t-12.71\t8\t100.00\t100.00\n+api-miR-279a\trna17432\t140.00\t-8.43\t7\t100.00\t100.00\n+api-miR-279a\trna27672\t166.00\t-22.87\t19\t78.95\t84.21\n+api-miR-279a\trna1959\t141.00\t-13.46\t18\t72.22\t77.78\n+api-miR-279a\trna4728\t144.00\t-9.08\t11\t81.82\t81.82\n+api-miR-279a\trna13584\t141.00\t-12.25\t18\t72.22\t77.78\n+api-miR-279a\trna24628\t145.00\t-10.53\t8\t100.00\t100.00\n+api-miR-279a\trna2789\t141.00\t-12.40\t8\t87.50\t100.00\n+api-miR-279a\trna12191\t142.00\t-8.00\t9\t88.89\t88.89\n+api-miR-279a\trna8229\t151.00\t-14.33\t18\t77.78\t77.78\n+api-miR-279a\trna2248\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna17489\t145.00\t-12.32\t8\t100.00\t100.00\n+api-miR-279a\trna19953\t148.00\t-10.97\t19\t73.68\t73.68\n+api-miR-279a\trna17076\t140.00\t-10.21\t7\t100.00\t100.00\n+api-miR-279a\trna19892\t141.00\t-22.51\t16\t75.00\t93.75\n+api-miR-279a\trna2222\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna2246\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna9635\t146.00\t-19.30\t23\t65.22\t65.22\n+api-miR-279a\trna17538\t140.00\t-10.64\t7\t100.00\t100.00\n+api-miR-279a\trna13747\t173.00\t-24.00\t18\t88.89\t88.89\n+api-miR-279a\trna21294\t151.00\t-14.51\t12\t91.67\t91.67\n+api-miR-279a\trna7335\t141.00\t-12.70\t8\t87.50\t100.00\n+api-miR-279a\trna13820\t160.00\t-19.91\t17\t82.35\t82.35\n+api-miR-279a\trna25648\t155.00\t-15.02\t18\t72.22\t72.22\n+api-miR-279a\trna16112\t140.00\t-8.46\t7\t100.00\t100.00\n+api-miR-279a\trna16112\t140.00\t-11.40\t7\t100.00\t100.00\n+api-miR-279a\trna28946\t143.00\t-12.06\t18\t66.67\t77.78\n+api-miR-279a\trna8223\t149.00\t-14.11\t18\t77.78\t83.33\n+api-miR-279a\trna16113\t140.00\t-8.46\t7\t100.00\t100.00\n+api-miR-279a\trna16113\t140.00\t-11.40\t7\t100.00\t100.00\n+api-miR-279a\trna14062\t145.00\t-9.64\t8\t100.00\t100.00\n+api-miR-279a\trna24995\t149.00\t-10.62\t12\t83.33\t83.33\n+api-miR-279a\trna28104\t159.00\t-13.59\t14\t85.71\t85.71\n+api-miR-279a\trna9665\t145.00\t-12.71\t8\t100.00\t100.00\n+api-miR-279a\trna9665\t142.00\t-22.76\t19\t78.95\t84.21\n+api-miR-279a\trna26200\t143.00\t-9.96\t17\t70.59\t70.59\n+api-miR-279a\trna8900\t145.00\t-12.71\t8\t100.00\t100.00\n+api-miR-279a\trna24277\t151.00\t-12.00\t14\t78.57\t78.57\n+api-miR-279a\trna181\t145.00\t-12.71\t8\t100.00\t100.00\n+api-miR-279a\trna6966\t140.00\t-10.61\t7\t100.00\t100.00\n+api-miR-279a\trna6605\t140.00\t-10.64\t7\t100.00\t100.00\n+api-miR-279a\trna14788\t141.00\t-8.46\t18\t66.67\t66.67\n' |
| b |
| diff -r 000000000000 -r 3f6cdc878f35 test-data/miranda.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miranda.out Thu Apr 12 10:53:04 2018 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+api-miR-3015c\trna27318\t146.00\t-13.54\t2 19\t600 620\t17\t64.71%\t88.24%\n+api-miR-3015c\trna14037\t141.00\t-16.27\t2 18\t217 237\t16\t68.75%\t81.25%\n+api-miR-3015c\trna15090\t140.00\t-11.77\t2 17\t218 238\t15\t66.67%\t86.67%\n+api-miR-3015c\trna25490\t145.00\t-12.86\t2 19\t396 417\t18\t66.67%\t88.89%\n+api-miR-3015c\trna23800\t163.00\t-15.96\t2 20\t1263 1283\t18\t72.22%\t83.33%\n+api-miR-3015c\trna28874\t141.00\t-13.48\t2 15\t388 410\t15\t80.00%\t86.67%\n+api-miR-3015c\trna5471\t145.00\t-17.38\t2 20\t640 659\t18\t72.22%\t83.33%\n+api-miR-3015c\trna16140\t142.00\t-15.04\t2 19\t1624 1644\t17\t64.71%\t82.35%\n+api-miR-3015c\trna16105\t141.00\t-16.02\t3 20\t377 396\t17\t70.59%\t88.24%\n+api-miR-3015c\trna142\t150.00\t-17.80\t2 19\t1445 1465\t17\t70.59%\t88.24%\n+api-miR-3015c\trna28003\t146.00\t-11.43\t2 16\t37 58\t15\t73.33%\t80.00%\n+api-miR-3015c\trna6629\t140.00\t-11.26\t2 19\t199 218\t17\t70.59%\t82.35%\n+api-miR-3015c\trna31159\t154.00\t-15.85\t2 19\t10 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