Mercurial > repos > iuc > mothur_make_contigs
changeset 1:3dab7d200c10 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
| author | iuc |
|---|---|
| date | Tue, 05 Sep 2017 17:14:01 -0400 |
| parents | 2b3fac454f43 |
| children | bfe5103b1e8f |
| files | make.contigs.xml test-data/test_forward.fastq test-data/test_reverse.fastq |
| diffstat | 3 files changed, 49 insertions(+), 7 deletions(-) [+] |
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--- a/make.contigs.xml Fri May 19 05:06:51 2017 -0400 +++ b/make.contigs.xml Tue Sep 05 17:14:01 2017 -0400 @@ -12,7 +12,9 @@ ## Symlinks creation or On the fly creation of a combo file #if $input_type.type == 'list_collection' #for $pair in $input_type.list_paired_collection: - echo -e "${pair.name}\t${pair.forward}\t${pair.reverse}" >> combo_fastq.dat && + ln -s ${pair.forward} `basename ${pair.forward}` && + ln -s ${pair.reverse} `basename ${pair.reverse}` && + echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat && #end for #elif $input_type.type == 'simple_collection' ln -s '$input_type.paired_collection.forward' ffastq.dat && @@ -177,17 +179,17 @@ </element> <element name="Pair2"> <collection type="paired"> - <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" /> - <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" /> + <element name="forward" value="test_forward.fastq" /> + <element name="reverse" value="test_reverse.fastq" /> </collection> </element> </collection> </param> </conditional> - <output name="fasta" md5="dab69a0e36f718b55d8defad26ec469b" ftype="fasta"/> - <output name="qual" md5="cdba5409e4f87e3cd093a4e51084d616" ftype="qual"/> - <output name="report" md5="80b992abd7e4d6a5e89fa70011ef2384" ftype="txt"/> - <output name="group" md5="2be2adb030c4fc001bfac7e1172b40e1" ftype="mothur.groups"/> + <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/> + <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/> + <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> + <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> <expand macro="logfile-test"/> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_forward.fastq Tue Sep 05 17:14:01 2017 -0400 @@ -0,0 +1,20 @@ +@M00967:43:000000000-A3JHG:1:1101:18327:1699 1:N:0:188 +NACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG ++ +#>>AABABBFFFGGGGGGGGGGGGGGGGHHHHHHHGGGHHHHHGHGGGGGGGHGGGGGGHHHHHHHHHHGGGGGHHHHGHGGGGGGHHBGHGDGGGGGHHHGGGGHHHHHHHHGGGGGHG@DHHGHEGGGGGGBFGGEGGGGGGGG.DFEFFFFFFFDCFFFFFFFFFFFFFFFFFFFFFFFFFFDFDFFFEFFCFF?FDFFFFFFFFAFFFFFFFFFFFBDDFFFFFEFADFFFFFBAFFFA?EFFFBFF +@M00967:43:000000000-A3JHG:1:1101:14069:1827 1:N:0:188 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG ++ +3AA?ABBDBFFBEGGEGGGGAFFGGGGGHHHCGGGGGGHFGHGGCFDEFGGGHGGGEGF1GGFGHHHHHGGEGGHHHHHFGGGGGGHHHHHGGGGCDDGHHGGGFHHHHHHHHCD@CCHGGGGHEHGGG@GFGGGGGGG@BGGGEGCEBFFFBFFB;9@EFFFEFFFFFFFFFFFFAFBBBFFFFFBBBFFFFBBBFFFFFFFFFFFBBBBBBBFFFFFFFFFDDFAFFFFF.AF9/FBBBBB.EAFFE?F +@M00967:43:000000000-A3JHG:1:1101:18044:1900 1:N:0:188 +TACGGAGGATGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGTTTAATAAGTCAGTGGTGAAAACTGAGGGCTCAACCCTCAGCCTGCCACTGATACTGTTAGACTTGAGTATGGAAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATTCTCTGGGCCAAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA ++ +BA@BBBABBFFFGGGGGGGGGGHGGGGGHHHHGHHHGGGGHHHGGGGGGGGGHGGGGGGFHFHHHFHHHHHHGFHHHHHHFHGGFGHHGGHGGHHFHHHHHHHHHHHHHHGHHHGHDHHHHHHHHHGHDGFFHHHDHHHHHHHHHHHHFHHHDGHHGGGGGHHHHHGGGGEGGGGGBF0BGGGGGGGGFFFGGGDGFFFFBCFBFFBFFBEEFFEFFFFFFFFBDA9EEFFF>DFFFFDDFFFADDFFFF. +@M00967:43:000000000-A3JHG:1:1101:13234:1983 1:N:0:188 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG ++ +BCBCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHGHHHGHGGGGGGHHHHHHHGHHGHHHGHHHHHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHHGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFAFFFFFFFFFFFFFFBFFFFFFFFFFEFFFF +@M00967:43:000000000-A3JHG:1:1101:16780:2259 1:N:0:188 +TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACG ++ +BBCCBFFCDFCFGGGGGGGGGGHGGGGGHHHHHHHHGGHFHHHGGGEGGHHHGGGGGGGEFGGGHHHHFHHHHGHHHHG/FGGGFGHFHHHGA?CGEHGGGHGHHFBGHHHGGHHHHDGHHFHFHHHHHEC0DDDEDAFFDDEGHHHHHEHHHHHEGGAFFGGGGBDGGGGGGFFFGGFFG.FFFFFFFFFFFFFFFDEFF@=FFFFFF.AFFEFFFFFFFDFFFBFF.:;F-@FFBDAFAAC.;9?FFE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_reverse.fastq Tue Sep 05 17:14:01 2017 -0400 @@ -0,0 +1,20 @@ +@M00967:43:000000000-A3JHG:1:1101:18327:1699 2:N:0:188 +CCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTCAACGGCTGTACGGGGTTGAGCCCCGCAATTTTACCGCTGACTTGGCAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCCCGCCTCCTCCGT ++ +BABBBFFFFFFFFGEGGGGGGGGHGGHHHHHGGGGGGHHHGGHGGGGGGEGHHGHHHHHHHG11EHEGCGGGHHHHGFGEHHHHGHHHHHHHHHFHHGGGCGHHHHHGGGGGGFHG@EGHHHHHHGFGGGGGGAGDGGGGGGFGHHGHHECDGGGGFGGGDFG:D-FFGGGGFCFBDFBFFFF.;--.BBFFFF/9B.;>-@DDF.-9B@DFFF/FFF/AFAB/B/B/FFF.AAFBA--@=F-.AA.;B.. +@M00967:43:000000000-A3JHG:1:1101:14069:1827 2:N:0:188 +CCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTCAACGGCTGTACGGGGTTGAGCCCCGCAATTTTACCGCTGACTTGGCAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGGTAAAGCTCGCATCCTCCGG ++ +BABBBFFFFFFFGGGGGGGGGGGHGGHHHHHHGGGGGHHHHFHGGGGGGFGHHGHHHHGHGGGGGHGGCGGGHHHHGGGDBGHHHFHHHHHHGHHHHGGGGGHHHEHGGGGGHHHGGGGHGHHHHGGGGGGHHEHGGGGG@FCCGHHHHGHGGGAGFBCEFGGGADGFGFGGFF;ADFFFFFBDFA>.BFFEFFFFFAFF;D..FFAA;BFEFFBBFFFF?EFFFFB/FDC-99B9FB/;AF-ABFFFF.- +@M00967:43:000000000-A3JHG:1:1101:18044:1900 2:N:0:188 +CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTCTTGGCCCAGAGAATCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCATTCTCCTCTTCCATACTCAAGTCTAACAGTATCAGTGGCAGGCTGAGGGTTGAGCCCTCAGTTTTCACCACTGACTTATTAAACCGCCTACGCGCCCTTTAAGCCCAGTGATTCCGGACAAAGCCCGCCTCCCCCG ++ +>AAABFFFFFFFGGGGGGGGGGGGGGGGGGHGGGGGGHHGHGGCEGEGGGHHFHFGGGGHHGGGGBFHHGHGGHGHGHEHH4FHHHGGGGGGHHHFHGGGGGHH3FHGFGGHHHFFHDFHFHHHHHHHFHHHHDFG2FFFHHHHFHHHHHGHHGHGG/000<CDDHC01<CE/<.C=DDGDDGHBC/CCGHBCGF00CGB-;:E.CFGAAFG?CF009:9E..;//BB/:/9.9-.::B.9---9:..9D- +@M00967:43:000000000-A3JHG:1:1101:13234:1983 2:N:0:188 +CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGCCTTGATCTTCCGCCTGCGCCCCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGT ++ +ABBBBFFBBFBBGGGGGGGGGGGHGGHGGHHHGGGGGHHHHHHGGGGGGGGHHHHHHHHHHGGGGHGGGGGHHGHHGGGGHHHHHGHHHHHHHHHHHGGGGGHHHHGGGGGGHHHGGGGHHHHFHGGGHGHHGHHHHHHHHDGHGHHHFHHGGGFDC<C.AGHC/C/C0GG//:GBB0CF9009??-..9;/0;;B90;.;D.C.B9.:-@-:F/BF//;EE./;::/9.@.A.B:.9.9;-999B99/.; +@M00967:43:000000000-A3JHG:1:1101:16780:2259 2:N:0:188 +CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTTGCTGTCCAGCAGACCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGTCTGCCTCTCCAGTACTCAAGAAACACAGTTTCAAATGCAGGCCACAGGTTGAGCCCGTGGTTTTCACATCTGACTTGCGTCCCCGCCTACACGCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCACCTACG ++ +>AABAFFFFFFFGGGGGGGGGGGGGGGGGHHHGGGGGGHHHGFHHHHHHHHBGHGGGGGHHGGGGFHHFHHEFHHHHHEHHFHHHFFGGGGGHHFHHGGGGGFHHHHHHHHHHHHHHHGHHHHHHHFHHHHHHHHHEHHHHHHHHHHHGGGHHHHGGGGHGFHHHFG<CFHGGCDC.EHGHHGFHHGG0CGHHHCD@BFGF?B?DGGGDCEFFFFFFFFB?EFFFF/BFFD;?FFFBD=AEEFB/FFFFF?