Mercurial > repos > iuc > mothur_fastq_info
view fastq.info.xml @ 3:22cac0572d4c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author | iuc |
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date | Fri, 06 Apr 2018 04:04:16 -0400 |
parents | 1aa945e00ef2 |
children | 22da6f6c5be8 |
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<tool profile="16.07" id="mothur_fastq_info" name="Fastq.info" version="@WRAPPER_VERSION@.0"> <description>Convert fastq to fasta and quality</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$fastq' fastq.dat && #if $oligo.add == "yes": ln -s '$oligo.oligos' oligo.oligos.dat && #end if echo 'fastq.info( fastq=fastq.dat, pacbio=$pacbio, format=$format #if $oligo.add == "yes": ,oligos=oligo.oligos.dat ,bdiffs=$oligo.bdiffs ,pdiffs=$oligo.pdiffs ,tdiffs=$oligo.tdiffs ,ldiffs=$oligo.ldiffs ,sdiffs=$oligo.sdiffs #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ## rename some outputs #if $oligo.add == "yes": && mv fastq.scrap.fasta scrap.fasta && mv fastq.scrap.qual scrap.qual #end if ]]></command> <inputs> <param argument="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/> <param argument="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/> <param argument="format" type="select" label="format of sequence"> <option value="sanger" selected="true">sanger</option> <option value="solexa">solexa</option> <option value="illumina">illumina</option> <option value="illumina1.8+">illumina1.8+</option> </param> <conditional name="oligo"> <param name="add" type="select" label="Use oligos file?" help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file."> <option value="no">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param argument="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/> <param argument="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/> <param argument="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/> <param argument="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/> <param argument="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/> <param argument="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/> </when> <when value="no"/> </conditional> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/> <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/> <data name="fastq_scrap_out" format="fastq" from_work_dir="fastq*.scrap.fastq" label="${tool.name} on ${on_string}: fastq scrap"> <filter>oligos</filter> </data> <data name="fasta_scrap_out" format="fasta" from_work_dir="scrap.fasta" label="${tool.name} on ${on_string}: fasta scrap"> <filter>oligos</filter> </data> <data name="qfile_scrap_out" format="qual454" from_work_dir="scrap.qual" label="${tool.name} on ${on_string}: qual scrap"> <filter>oligos</filter> </data> </outputs> <tests> <test> <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> <param name="pacbio" value="false"/> <param name="format" value="sanger"/> <param name="oligo|add" value="no"/> <output name="fasta_out" ftype="fasta"> <assert_contents> <expand macro="test-fasta-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> <output name="qfile_out"> <assert_contents> <expand macro="test-qfile-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> <param name="pacbio" value="false"/> <param name="format" value="sanger"/> <param name="oligo|add" value="yes"/> <param name="oligos" value="GQY1XT001.oligos"/> <param name="bdiffs" value="1"/> <param name="pdiffs" value="3"/> <param name="tdiffs" value="3"/> <param name="ldiffs" value="3"/> <param name="sdiffs" value="7"/> <output name="fasta_out" ftype="fasta"> <assert_contents> <expand macro="test-fasta-format"/> </assert_contents> </output> <output name="qfile_out" ftype="qual454"> <assert_contents> <expand macro="test-qfile-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/> </assert_contents> </output> <output name="fastq_scrap_out" ftype="fastq"> <assert_contents> <expand macro="test-fastq-format"/> <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> <output name="fasta_scrap_out" ftype="fasta"> <assert_contents> <expand macro="test-fasta-format"/> </assert_contents> </output> <output name="qfile_scrap_out" ftype="qual454"> <assert_contents> <expand macro="test-qfile-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> <param name="pacbio" value="false"/> <param name="format" value="sanger"/> <param name="oligo|add" value="yes"/> <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/> <param name="bdiffs" value="1"/> <param name="pdiffs" value="3"/> <param name="tdiffs" value="3"/> <param name="ldiffs" value="3"/> <param name="sdiffs" value="7"/> <output name="fasta_out"> <assert_contents> <expand macro="test-fasta-format"/> </assert_contents> </output> <output name="qfile_out"> <assert_contents> <expand macro="test-qfile-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/> </assert_contents> </output> <output name="fastq_scrap_out"> <assert_contents> <expand macro="test-fastq-format"/> <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> <output name="fasta_scrap_out"> <assert_contents> <expand macro="test-fasta-format"/> </assert_contents> </output> <output name="qfile_scrap_out"> <assert_contents> <expand macro="test-qfile-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The fastq.info_ command reads a fastq file and creates a fasta and quality file. .. _fastq.info: https://www.mothur.org/wiki/Fastq.info ]]></help> <expand macro="citations"/> </tool>