Mercurial > repos > iuc > mothur_make_fastq
diff make.fastq.xml @ 2:2a3cc9dcd6fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:00:47 -0400 |
parents | c49147967884 |
children | 4287ded138de |
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--- a/make.fastq.xml Tue Sep 05 16:53:28 2017 -0400 +++ b/make.fastq.xml Tue Mar 20 22:00:47 2018 -0400 @@ -7,22 +7,22 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$qfile" qfile.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$qfile' qfile.dat && - echo 'make.fastq( - fasta=fasta.dat, - qfile=qfile.dat - #if $chooseformat.use == "yes": - ,format=${chooseformat.format} - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'make.fastq( + fasta=fasta.dat, + qfile=qfile.dat + #if $chooseformat.use == "yes": + ,format=${chooseformat.format} + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> @@ -41,6 +41,7 @@ </when> <when value="no"/> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -59,7 +60,13 @@ <test><!-- test defaults --> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> - <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/> + <output name="fastq" ftype="fastqsanger"> + <assert_contents> + <expand macro="test-fastq-format"/> + <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> + </assert_contents> + </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with quality score format conversion --> @@ -67,22 +74,27 @@ <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> <param name="use" value="yes"/> <param name="format" value="illumina"/> - <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/> + <output name="fastq" ftype="fastqillumina"> + <assert_contents> + <expand macro="test-fastq-format"/> + <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> + </assert_contents> + </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** -The fastq.info_ command reads a fasta file and quality file and creates a fastq. +The make.fastq_ command reads a fasta file and quality file and creates a fastq. -.. _fastq.info: https://www.mothur.org/wiki/Make.fastq -]]> - </help> +.. _make.fastq: https://www.mothur.org/wiki/Make.fastq + + ]]></help> <expand macro="citations"/> </tool>