Mercurial > repos > iuc > mothur_degap_seqs
diff degap.seqs.xml @ 0:7cd72305d496 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:09:06 -0400 |
| parents | |
| children | f643cbd3a967 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/degap.seqs.xml Fri May 19 05:09:06 2017 -0400 @@ -0,0 +1,52 @@ +<tool profile="16.07" id="mothur_degap_seqs" name="Degap.seqs" version="@WRAPPER_VERSION@.0"> + <description>Remove gap characters from sequences</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 "$fasta" fasta.dat && + + echo 'degap.seqs( + fasta=fasta.dat + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/> + </outputs> + <tests> + <test> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> + <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed. + +.. _degap.seqs: https://www.mothur.org/wiki/Degap.seqs + +v1.21.0: Updated to Mothur 1.33 + +]]> + </help> + <expand macro="citations"/> +</tool>