Mercurial > repos > iuc > mothur_make_contigs

changeset 1:3dab7d200c10 draft

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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(-) [+]
line wrap: on
line diff
--- 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?