Mercurial > repos > iuc > mothur_make_contigs
diff make.contigs.xml @ 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 |
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>