| Previous changeset 6:2bc40bfbcfb4 (2023-10-16) Next changeset 8:9da9706f7ca9 (2024-01-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit be3f3d0eb7e565cea414babb410e6ae32875c5f2 |
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modified:
maxbin2.xml |
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added:
test-data/test4_reads 2.fastqsanger |
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| diff -r 2bc40bfbcfb4 -r 28a0b1446d2b maxbin2.xml --- a/maxbin2.xml Mon Oct 16 07:46:13 2023 +0000 +++ b/maxbin2.xml Wed Dec 20 20:27:57 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4"> +<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy5"> <description>clusters metagenomic contigs into bins</description> <macros> <token name="@MAXBIN_VERSION@">2.2.7</token> @@ -30,7 +30,7 @@ #if $assembly.type == 'individual' ## uncompress .gz reads files if necessary #set $e = $assembly.inputs.reads - #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) + #set $identifier = re.sub('[^\w\-\\.]', '_', str($e.element_identifier)) #if $e.ext.endswith(".gz") gunzip -c '$e' > '$identifier' && echo '$identifier' >> reads_list && @@ -394,6 +394,38 @@ <output name="noclass" file="4/out.noclass" ftype="fasta" /> <output name="toshort" file="4/out.tooshort" ftype="fasta" /> </test> + <!-- test w contigs and reads in fastqsanger format as input (and whitespace in reads filename)--> + <test expect_num_outputs="4"> + <param name="contig" value="test4_contigs.fasta" ftype="fasta" /> + <conditional name="assembly"> + <param name="type" value="individual"/> + <conditional name="inputs"> + <param name="type" value="reads"/> + <param name="reads" value="test4_reads 2.fastqsanger" ftype="fastqsanger"/> + <param name="output_abundances" value="false"/> + <param name="reassembly" value=""/> + </conditional> + </conditional> + <section name="adv"> + <param name="min_contig_length" value="1000"/> + <param name="max_iteration" value="50"/> + <param name="prob_threshold" value="0.5"/> + </section> + <section name="output"> + <param name="plotmarker" value=""/> + <param name="marker" value="false"/> + <param name="markers" value="false" /> + <param name="log" value="false"/> + <param name="markerset" value="107"/> + </section> + <output_collection name="bins" type="list" count="2"> + <element name="001" file="4/out.001.fasta" ftype="fasta"/> + <element name="002" file="4/out.002.fasta" ftype="fasta"/> + </output_collection> + <output name="summary" file="4/out.summary" ftype="tabular" /> + <output name="noclass" file="4/out.noclass" ftype="fasta" /> + <output name="toshort" file="4/out.tooshort" ftype="fasta" /> + </test> <!-- test w contigs and reads in fastqsanger.gz format as input --> <test expect_num_outputs="4"> <param name="contig" value="test4_contigs.fasta" ftype="fasta" /> |
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| diff -r 2bc40bfbcfb4 -r 28a0b1446d2b test-data/test4_reads 2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_reads 2.fastqsanger Wed Dec 20 20:27:57 2023 +0000 |
| b |
| b'@@ -0,0 +1,1948 @@\n+@NC_006347.1_63\n+AAGCCTTGGCCGGAAATATTTTATTTTGCTTTGTCGGCTACACAGTCCGAACTGCGTGATTCGCTAATGATAGGTGATAGTTGGGAAGCGGATATTACAGGTGCCAATGGCATAGGGATGCATCAGATCAGTCATACCATGGGTGATGGTCAAAAAGACAGGCATTGTTCCCAAGGGGTTAGTCAACGTAAAGAAAGAGGTAAAACAGAGTAAAGCGAAAGGTAAGAGAGTGTCCATAGTTGTATTTTTATG\n++\n+BBBBBFFFFFFFFFFFFFBFFFFFFBFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFB/FFFFFFFFFFFFFFF<FBFFFFFFFFFFBFF<FFFFBFFFFFFFFFFFFF<F/FFFFF</FFFFFFBBBBBFFFFFF<FFFFFF/FFFFFF/FFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFF<FFFFFFFFBFFFFFFFF/FFFFF7BBFFBFFFF\n+@NC_006347.1_193\n+GGAGGAGTAAAACCCTATACCGTAAGTAGCAATTCTGATATCCTCAAAGTGAATATGGATAAGCTTTCGGATGCTTTCAACTACGAAACACTGGGCGTTGGTGATGCGGAAGTGACTATTACCGATCTTATCTCACTCAAAGCCGGAGGTGTAGGCCTCAACCTGACACAGGCAGACTATGTATTCATTATCGATCCTTGGTGGAACCCGGCAGCCGAATCACAGGCCATCGCCCGAGCCCACCGTATCGGA\n++\n+BBBBBFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFF/FFFFFFFFFF<FFFFFFFFFFFFFFFFFFF/BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<<FFFFFFFBFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFF<F<FFFFFFFFFFFFBF/FFFFFFFFFFFFFFFFFFF/FF/FFF\n+@NC_006347.1_656\n+GTTATACTTTACCAATTGCTTGTTGCTACAGCGGGAGAGACTTATGAATTCACTTCTTGTTGGAGTACGCCAACCACTACCGTATATACTTTCGTCAAGACGTGTACAAGGATCAACAGCACCATACTCCACATCATGGAAGATCGGTCCTTCGACCAATGTGGTAGCCGCCAACACAAATAATACGGCGGCATTCAGTCCGAACACGACCCTGAATACAACCATACGCATGGTTCCATTTGCAGGGGCCAG\n++\n+BBBBBFFFFFFFFBFFFFFFFFFFFFFFBFFFBFFFFFFFFFBFFFFFFFFFFFFFFF/FF<FFBFFFFFFBFFF<FFFFFFFFFFFFF/FFFFFBFFFFFFFFFFFFFFFFBFFFFFFFFFFBFFBBBBBFFFBBFFFFFFFFFFFFFFFFF/<FFFFFFFFFFFFFFFFFFFFFFFF/FFBFFFFFFFFFFFFFFFFFF/FFFB<FFFFF/FFFFFFFFFBFFBFFFFFFFFFFFFFFFFFF7FF<FF/F\n+@NC_006347.1_1720\n+CATTACCGTAGTCGAAGTGGTCGGAGTCATCCCCAGGGTACAAACTTCGGCAGGATGTCCTGTGCTCAGGCATACATCCGATTCGCTGGCAAGCGGACTGTCCGGATTGCCGGTGATGACAATGAAACGGGTTCCGGCATCTACGGCAAATCCGCAATAAGCCACCTTCGAAGAAGAGGGTTCATGAATAATGCGAAGTCCATTGGACAGGGTATGTATATTATATTGCATTTCTGCACGGGTACTTAACTG\n++\n+/BBBBFFFFFFFBFFFFFFFFFF<FFFFFFFFFFFFFFFFFFBFFFFFFFF/FFFBFFFFFFF/FFFBFFFFFFFFFFFFFFFFFFFFFF<FFF/F<FFBFBFFFFFF<FFFFFFFFF7F7FBBFF/BBBBFF<FFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFBFFFFFFFF<FFFF<FFFFFFFFFFFFFFFFFFFFFFFFFF<FF/FFFFFF/FFFFF/FF\n+@NC_006347.1_2535\n+CAGGTAGCACAGGAATGTTACACATGATTTTAGTCTTTTGGCGGTTCTTCCTTATCCAAAGTTCCCCTTTATTGTCTTTTACCAAGTGTTCAGGTGATAAGTCTTTCACATCGCTGAACGCCAAACCGGATCACTGAAAACAAAAGAAAAATCAAGCAAATCCCTGATAATCAGACATTATCAGGGATTTCTTTTTTCCGGCAGGTGGCAGAAAACAGCCGTTTCAAGCATATTATTGGTGGATAAATCGTG\n++\n+BBBBBFFFFFFFFFFFBFFFFFFFFFFFFF<FFFFFFFFF/FF/<FFFFFFFFF/FFFFFFFFFFFFFBFFF/FFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFBFF<FFF7FFBFFFFFFBBBBBFBFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFBFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFBFFFFBFBBF/FFFF<FFFFFF7F\n+@NC_006347.1_3006\n+GAACTGTTACTGCGTTTGAAAGCTAATCATCTGGCTCCGGCAATGCATCCCGTATCTACCGCTTTTTATCAGATTCCCGAGAATAAGCTCGTAGCAGATACGTTTGCCATTGTTATGGGCTCCAGCCGATATCATAAGCCATATCGAGAAAAAACGATACTTGTGCCTCAGCCCCTTTCAGGTCTCCACAGTTTGCCAACCAGATACGGTCGGCCGTAGTATCATACGCTTTGCGAAGCTCTTCATACATTA\n++\n+BBBBBFFBFFFFFFFFFFFFFFFFFFF<FFFBFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFF<FFFFF</FFFFFFFFFFF<FFFFFF<BFFFFFFFFFFBFFFF/FFBFFFFFFFFFB7FFFBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFBFFFFF<FFFFFFFFFFF/FFFFFFFFFFFFF7FBFFFFFFFFFFFFFFFBFFFFFFFFFFFFB\n+@NC_006347.1_3200\n+AGCAGACAATCATCAATATACTCGTTTTTTTTTTCTCTTTTCCAATTCATAAATAATTAGCACAAATGTACGAAATGTGTTCGTAATCGCAAATTATTTATTATGAAAGATATAGAATTTATCAAGCCAAACAAGGCTTTAAGTGGTAATAATCCCTTTTCTACTTGTGAAACAAGGTATATTCCAAGTCTGAAACGGAAATGCCAAGCCCTTTGGGTTTTAGAAGATTTCTTCTTTTTCGCTTACAAGAAG\n++\n+BBBBBFFFFFFFFFFFF<FFFFFFFFFFBFFFFFFFFFFFFFFFFFFF/FFFBFFFFFF<FFFFFFFFFFFFFFBFFFBFBFFFFFBFFFFFFF<FF/F/FFFFB/FFF<FFFFFFFF<BFF/FF/BB<</BFF/FF<FFF7FB<FFFF//BFBF<FF//<F<F/</<F/<FFFFFF/BF//FB/<FBFB/F/F///B<FBFFF//<<B/BB//F/FBF7<FB<B/FFFF/F/B7BF7F/BB/<B7/F/BBF\n+@NC_006347.1_4206\n+TTCGCCCGTATTCGTCTCTATTCCTTTCACTTCTCCCTGTTCGATGATCAATGCATCCATCCGTGTCTTGAAGTGTACTTCGCCTCCACATTCAATAATCGTATTGCGCATATTCTCTATCACCCGCCGCAGGTTATTGTGGTAGGTGCAGGCCCCGGAGGACTGTTTGCCGCATTACGGCTGATAGAACTGGGGCTGCGTCCTGTCGTCGTGGAGCGTGGCAAGGATGTGCGCGAACGTAAGAAAGACCTG\n+'..b'AGGAGATAATAGCCGAATCGGGCT\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF<FFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFF<FFFF//FFFBFFF/FBB/BBF///FF/<F</BB</FF//FF<F<F///FF////7BB/F//BF/</FF//FFB<///<<//F/<<BF/</F/FB/<FF/FF<77/F</FF</7/7B</<FB/B/B//<F/FFF/77</<F/\n+@NC_006347.1_12312\n+CCGTGAGGTGAAGAAGCTAATCTTAGACTAAACCATCTGAAAATCAATATCTTTAAGAAGTAAGATTTCTGTCCTCAAAAGCTTTGTTTTAACACAGAGTTAAAGCTTGTTCTTTGGATGTGAATACCATCGTGCTTGAAGTTCCACCACAGGCCCCCCCTTTCTTTATCATACGACTCTTTCCAGACATGGTAGAATCCCGAAGAGGCATGTGCCAGGTATTTCGGGTCATTCGTGATTTCGTAAGCACGT\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFF/FFFB/FFFFFFFFFFFFFFFFFF//FFFFBFFFFFFBFFFFFFFFF<FFFFF//FBBBBBFF/FFFBFFFFBFFFFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFBBF<FFFFFFFFFFF7FFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF<FFFBFFFFF/\n+@NC_006347.1_13121\n+TTGTAGGTGTACTTGTAGTTCCCCTCGACCACGAAGCGGTTGTCGGTGAACTCCAATCCCTCTTTGAGTATCCTTTCGCTCACCACCTTTATCGGAAAACCGTAAAGTTCACCGACCTGCGTGTACCTGTTCGGGCTCTACCTCTATGCTCGGAACGGGTGTGAACGCCCAGAAACGGTGTGTGGCTATCCATCATCTCGATACGCCGTGGCGACCGTCCGACTTGCAACAGCGTGACGGACGCGGAGTTAG\n++\n+BBBBBFFFFFFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFBFFFFFFFFF/FFFF/FFFF<F<FFFFF/F<FBF/FFBBFFBFBFBFFFFFFFFFFFFBBBBBFFFFFFFFFFFFFBFFFFFFFFFFFFF<FFFFFFFFBF7FFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/BFFF/F<FBFF/FFFF/FFBF\n+@NC_006347.1_13826\n+GCAGGAACAGCAAGTCAAGATAGCCACGCTCCAGCAAAGCCTCGAACGGTATAAGTCTTACGATGAAATGAGCCGGAAAATTATCCCGGAACTGAAAGTACTCTATCCGTCGGTGACGGCTTTGTCTGTATCCATCCAATGTGATGGGAGCCACGTATTCGGGACGATAGGGCACGTTGTCGGGTGAATAGTCGGCAGGACGGTTGTCTTTACCGGCATAGATACGAAAGACGCAGAAATCGCCAGTATGAC\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFBFFFFFFF/FF</FBFBFFFFBFFFFFFFFFFFFFFFFFFFFF7FFFFFFFFFFFFF7FFFFFBF<FFF/BBBBBFFFFF/FF<FFFFFFFFFFFF<BF/<FFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFF<FF<FFFFFBFFFFFFFFFFFFBFFF\n+@NC_006347.1_13843\n+TCTTATTTATTTTCGCCAGTTCCGATTTTACGGATTCAGGGGCTTCGGATGGGTTGATATGTGCCTTATCTATATATCCGAACGCCAATATTACAACTTCACTCTTTTTCAGTGAATAACGTTTGCCTTTAGCGTGTTACAAGAACACGCTGTAATGACACCTGTAATAAGTATTTTCTTTGTAATGCTTATTATCAGGTATTTATCTATTCATATTTCTATAAAAAAGTAATTACCATGCCAAACAGCAGT\n++\n+BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFF<FFFF<FFFFBFFFF<FFFFFFFFFBFFFFFFFFFFFFBFFFFFFFFFFFFBFFFFFF/FBFFFFFFFFF7FFF<FFBFBFFFFFFFFFFFFF/FB<BBBFFFFF<BFFBBFF<FFFFFFFFFFFF<FFFFFFFFFFFFFFFFF/<FFFFFFFFFBFFFFFFF/FFFFFF<FFFF7FFFFFFFFFFFF/FFFF<FF/FFFFBFFFFFFFFFFFFFFBFFF/\n+@NC_006347.1_13966\n+TTTTACGGCAGTAGTGACCGCCACCCCGTTATTTACGGGCTGTAGAGCACTGCTTTTCTGGGTACCGAATACCAAAAACAACAGGCATAACATTAGTAGTTTGATGTATGCTGCCATAATTGGCGGACAGCCAACTTCTTTATCCGGTACAAATACAGATTCCACAGATTAACACAGATTCCCCACTAGGACAATCAATCTCTGCTAATCTGTGGAAGCAATAGTATATCGACAAATATACAAGGTTTGTAC\n++\n+BBBBBBFFFFFFFFFFFFFF<FFFFFFFFFFF<FFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFBF/FFB<FFF<FFFF<FFFFBFFFFFBFFBBBBBFFFFFFFFFFBFFFFFFFFFFFBFFFFFFFFFFFFFFFFFBBFF/FFFFFFFFF/FFFFFFFFFFBFFFFFFFFBFFFFFFFFF/F/BFFFFFFFFBBBFFFBFF/FFFBFBFBFF/FFFF\n+@NC_006347.1_14109\n+GCCGGGGATGGTAATTTCCTCTTTTTCCTCGCCATAGACGGCACGCCATCCGGTTTGCTTCACGACGCTGCCTTTTACGGTAAACTCCACTCCGGCACATTCCGCCGTGACAGTGGTCACATCCTTTCTACCTCGCCGCCAAAGCGCGGAGCGAATCCGACTGGCTCGTGGGCATCAACGGCACACAGGCGTTATCCATCGCCGCCGGACACGGCACGTATTCCGTGGGGCGGGTGCAGACACCAACGTTGG\n++\n+B<BBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFF<FFFFBFFFFFFFFFFFFFFFFFFFFFBFFFF<FFFFFBFFFFFFFF/FFFF/FFFFF/BFFFFFFFF<BBBBBFFFFFFFFFFFFFF<FFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFBFFF7\n+@NC_006347.1_14401\n+AAGAAGGATTCAAGACTCCGGTGGGAAAGTTACCGTTGGACAAACAACTGGAGAATTCATGGGAAAAACAGATGGAAATTGATATGAATGGCAATCCATACTGGTATATTGCCACATCAAGAGTGATTTATCCAGTTCCTTAGCCAATTCCGGTGATTTTTTAGCCAATTCTTCGCTAAGTGCTTTGACAGCTACTTTGTTTGCAGCTTCCAGGCTATAACCGATGGTTACCATTACCTCTACATTTTTGTA\n++\n+BBBBBFFFFFFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FF/FFBBFFFBFFFFFFFFFFBBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFBF<FFFFF/FFFFFFFFFFFFFFFFFFFFF/FBFFFFFFFFFF<F<FFF/\n' 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