| Next changeset 1:c172fed9eb75 (2017-11-12) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit d18a08287799b0aa6ca50242ebcc218820923fb2-dirty |
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added:
gotohscan.xml test-data/C0299.fa test-data/NC_000913.fna test-data/gotohscan.result1 tool_dependencies.xml |
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| diff -r 000000000000 -r 6845ddcd5588 gotohscan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gotohscan.xml Thu Jul 02 12:06:30 2015 -0400 |
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| @@ -0,0 +1,103 @@ +<tool id="rbc_gotohscan" name="GotohScan" version="1.3.0"> + <description>Find subsequences in db</description> + <requirements> + <requirement type="package" version="1.3">gotohscan</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> + <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/> + </stdio> + <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command> + <command><![CDATA[ + GotohScan + + -d $dbase + -q $query + + #if $split and $split is not None + --split $split + #end if + + #if $e and $e is not None + -e $e + #end if + + #if $p and $p is not None + -p $p + #end if + + $s + -o $o + > + + #if $o.value == '0' + $output0 + #elif $o.value == '1' + $output1 + #elif $o.value == '2' + $output2 + #elif $o.value == '3' + $output3 + #elif $o.value == '4' + $output4 + #elif $o.value == '5' + $output5 + #end if + ]]></command> + <inputs> + <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/> + <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/> + <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/> + <param argument="-e" name="e" type="float" optional="true" label="E-value" help="Value should be < 10. default: 1e-3"/> + <param argument="-p" name="p" type="float" optional="true" label="Percent identity of aligned sequences" help="Value should be in [0.0,100.00]"/> + <param argument="-s" name="s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Print score distribution data for each query to a file"/> + <param argument="-o" name="o" type="select" label="Output Format"> + <option value="0" selected="true">Blast tabular output</option> + <option value="1">Blast tabular output + aligned sequences</option> + <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option> + <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option> + <option value="4">BED + aligned sequences</option> + <option value="5">GFF + aligned sequences</option> + </param> + </inputs> + <outputs> + <data name="output0" format="tabular" label="${tool.name} on ${on_string}"> + <filter>o == '0'</filter> + </data> + <data name="output1" format="tabular" label="${tool.name} on ${on_string}"> + <filter>o == '1'</filter> + </data> + <data name="output2" format="fasta" label="${tool.name} on ${on_string}"> + <filter>o == '2'</filter> + </data> + <data name="output3" format="maf" label="${tool.name} on ${on_string}"> + <filter>o == '3'</filter> + </data> + <data name="output4" format="bed" label="${tool.name} on ${on_string}"> + <filter>o == '4'</filter> + </data> + <data name="output5" format="gff" label="${tool.name} on ${on_string}"> + <filter>o == '5'</filter> + </data> + </outputs> + <tests> + <test> + <param name="dbase" value="NC_000913.fna"/> + <param name="query" value="C0299.fa"/> + <param name="o" value="2"/> + <output name="" ftype="fasta" file="gotohscan.result1"/> + </test> + </tests> + <help> +<![CDATA[ +**GotohScan** is a search tool that finds shorter sequences +(usually genes) in large database sequences (chromosomes, genomes, ..) +by computing all semi-global alignments. Thus, the query sequence is +never truncated or split into subsequences, but always mapped to the +database over its complete length. The alignment is computed via the +Gotoh-alignment algorithm using affine gap costs. +]]></help> + <citations> + <citation type="doi">10.1093/nar/gkn1084</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 6845ddcd5588 test-data/C0299.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/C0299.fa Thu Jul 02 12:06:30 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>C0299 1763522:1763600(EDL933) 1230629:1230707(MG1655) +gccgcgtgagcacaggataagagaacgaaaaatcagcagtctatgcagcgacaaatattgatagcctgaatcagtattg |
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| diff -r 000000000000 -r 6845ddcd5588 test-data/NC_000913.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_000913.fna Thu Jul 02 12:06:30 2015 -0400 |
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| b'@@ -0,0 +1,66311 @@\n+>gi|556503834|ref|NC_000913.3| Escherichia coli str. K-12 substr. MG1655, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG\n+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA\n+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG\n+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT\n+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT\n+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG\n+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC\n+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT\n+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC\n+CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC\n+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG\n+CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA\n+ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC\n+TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG\n+TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT\n+CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG\n+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA\n+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG\n+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA\n+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC\n+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG\n+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT\n+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG\n+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA\n+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT\n+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG\n+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA\n+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC\n+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG\n+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT\n+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC\n+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC\n+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC\n+AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC\n+ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT\n+ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG\n+CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC\n+GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG\n+GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC\n'..b'GAGGTTAACGTTGC\n+TGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAG\n+AGCGGTTGCATCACGCTAAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTA\n+GTGGTATTCCTGACTACGCGCTTTCACGTATTTTTGAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCA\n+AAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTG\n+CGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTC\n+TTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTG\n+GAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGATTCGGCAGGTGATT\n+GTCGAACGTGCTGATTACCGTAGCGATGTGGAAGATGCGATTCGCCAAAGTACCAGCGGGCCGCAAAAAC\n+TCGTTGGGCCGCTCATCGCTATTCCTGTGACCGAGCTTTATACGGTGCAGGAAGAGGATAAAACCGTGGA\n+GCGGAAACGAAGTTTTATCCATTTTTGGTTACCTGAGTCATTGATGGTTGATGGCAATCAGAACGTGGAA\n+GAACGCAAGATAGGGATTTATACCGGTCAGGTCTGGCACAGTGATTTAACGTTAAAAGCCGATTTCGATG\n+TTTCGCGTCTTAGCGAACTCAACGCGCCAAATATCACCTTAGGCAAGCCATTTATTGTGATTAGCGTCGG\n+GGATGCGCGTGGTATTGGTGTGGTGAAAGCGCCTGAAGTTAACGGAACGGCGCTGACCATTGAACCCGGC\n+ACCGGGTTAGAGCAAGGCGGGCAGGGCGTGCATATCCCTTTACCTGAAGGGGACTGGCGGAAGCAGAACC\n+TGAAGCTGAATATGGCCCTGAATTTAAGCGGTACCGGCGATCTTTCTGTGGTGCCTGGCGGGCGTAATAG\n+CGAAATGACCTTAACCAGCAACTGGCCGCATCCCAGTTTTTTAGGTGATTTTCTACCAGCCAAACGGGAA\n+GTTAGCGAGTCAGGTTTTCAGGCGCACTGGCAAAGCAGCTGGTTTGCTAATAATCTCGGTGAGCGTTTTG\n+CTTCAGGCAATGATACCGGCTGGGAAAACTTCCCGGCGTTTAGCGTCGCAGTAACGACGCCAGCCGATCA\n+ATACCAATTAACTGACCGGGCGACTAAGTACGCCATTCTGCTGATTGCACTGACTTTTATGGCGTTCTTT\n+GTTTTTGAAACGCTCACCGCGCAACGTTTACACCCAATGCAATATTTGCTGGTGGGGCTTTCATTGGTGA\n+TGTTTTATTTGCTCTTGCTGGCGCTTTCTGAACATACCGGTTTTACCGTGGCATGGATAATCGCCAGTCT\n+GATTGGGGCGATAATGAACGGTATTTATTTGCAAGCGGTATTGAAAGGTTGGTGCAACAGCATGTTGTTT\n+ACCCTCGCGCTGTTGTTGCTGGATGGTGTGATGTGGGGACTGCTCAACTCTGCCGATAGCGCGCTGTTGT\n+TGGGAACCAGTGTGCTGGTGGTGGCGCTGGCCGGCATGATGTTTGTGACCCGTAATATCGACTGGTATGC\n+GTTTTCACTGCCGAAAATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAA\n+GGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCA\n+GATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTC\n+GAAATGTTTACGAATACGGCGGATCGTCACGTCTACAGTACGGTCGTGCGGTTTCAGCTCACGGCCGGTC\n+ATTTTCTTCAGCAGTTCAGCACGGGACTGAATTTTGCCTGGGTTTTCACAGAAGTGAAGCATGGCGCGGA\n+ACTCGCTGCGCGGCAGCTTGTACTGCTCGCCATCAGGGCCGATCAACGAACGGCTGTTGATGTCCAGTTC\n+CCAACCATTGAACTTGTAGCTTTCAACGCTACGACGTTCTTCGCTGACAGTACCCAGATTCATGGTACGG\n+GACAGTAGGTTGCGTGCACGAATCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCAC\n+CGATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGC\n+CTGCTCGCGCAGTTCACGCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGG\n+TTGATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTT\n+CCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGT\n+CTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGAT\n+GCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCC\n+ATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGG\n+CTGTCATCCTAACCATTTTAACAGCAACATAACAGGCTAAGAGGGGCCGGACACCCAATAAAACTACGCT\n+TCGTTGACATATATCAAGTTCAATTGTAGCACGTTAACAGTTTGATGAAATCATCGTATCTAAATGCTAG\n+CTTTCGTCACATTATTTTAATAATCCAACTAGTTGCATCATACAACTAATAAACGTGGTGAATCCAATTG\n+TCGAGATTTATTTTTTATAAAATTATCCTAAGTAAACAGAAGGATATGTAGCATTTTTTAACAACTCAAC\n+CGTTAGTACAGTCAGGAAATAGTTTAGCCTTTTTTAAGCTAAGTAAAGGGCTTTTTCTGCGACTTACGTT\n+AAGAATTTGTAAATTCGCACCGCGTAATAAGTTGACAGTGATCACCCGGTTCGCGGTTATTTGATCAAGA\n+AGAGTGGCAATATGCGTATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGC\n+GCGGGCAATGAAAACGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCC\n+ACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAAT\n+CGTTACACGATGTCGATTTCACTGTCGCCACCACTGCGCGCAGTCGGGCGAAATATCATTACTACGCCAC\n+GCCAGTTGAACTGGTGCCGCTGTTAGAGGAAAAATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGT\n+CGCGAAGATTCCGGGTTGACTAACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGG\n+CGGATTATCCTTCGCTCAATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAACATTAATACA\n+ACAACCGGCGAAAAGTGATGCAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAGCCATGACA\n+TTGCTGACGACTCTGGCAGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTT\n+TAGAGCAACGAGACACGGCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAAAA\n+AACGCCTTAGTAAGTATTTTTC\n' |
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| diff -r 000000000000 -r 6845ddcd5588 test-data/gotohscan.result1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gotohscan.result1 Thu Jul 02 12:06:30 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>C0299:gi|556503834|ref|NC_000913.3|:1230628-1230707:+:96.20:4.292591e-15 +GCCACGUGAGCACAAGAUAAGAGAACGAAAAAUCAGCAGCCUAUGCAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG |
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| diff -r 000000000000 -r 6845ddcd5588 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 02 12:06:30 2015 -0400 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="gotohscan" version="1.3"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/GotohScan/GotohScan-1.3.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>GotohScan</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="GOTOHSCAN_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency> |