Mercurial > repos > iuc > mothur_fastq_info
diff fastq.info.xml @ 2:1aa945e00ef2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:01:25 -0400 |
| parents | 19316e7c4802 |
| children | 22da6f6c5be8 |
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--- a/fastq.info.xml Tue Sep 05 16:52:35 2017 -0400 +++ b/fastq.info.xml Tue Mar 20 22:01:25 2018 -0400 @@ -7,60 +7,65 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@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 +## 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 $oligo.add == "yes": - && mv fastq.scrap.fasta scrap.fasta - && mv fastq.scrap.qual scrap.qual - #end if +echo 'fastq.info( + fastq=fastq.dat, + pacbio=$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 name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/> - <param name="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 name="format" type="select" label="format of sequence"> + <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."> + <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 name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/> - <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/> - <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/> - <param name="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 name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/> - <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/> + <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"/> @@ -81,50 +86,108 @@ <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> <param name="pacbio" value="false"/> <param name="format" value="sanger"/> - <param name="add" value="no"/> - <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/> - <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/> + <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="add" value="yes"/> + <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" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/> - <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3" ftype="qual454"/> - <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933" ftype="fastq"/> - <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/> - <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01" ftype="qual454"/> + <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="add" value="yes"/> + <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" md5="88c573d00181be6dd519a0c9599f8b0c"/> - <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/> - <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933"/> - <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c"/> - <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01"/> + <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[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -134,7 +197,7 @@ .. _fastq.info: https://www.mothur.org/wiki/Fastq.info -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>