Mercurial > repos > bcclaywell > microbiome_pplacer_suite
diff alignment.xml @ 3:221a97bf686d draft
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author | bcclaywell |
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date | Wed, 25 Mar 2015 16:39:10 -0400 |
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children | 3c50a937d7c1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignment.xml Wed Mar 25 16:39:10 2015 -0400 @@ -0,0 +1,47 @@ +<tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0"> + <description>with sequences in a reference package</description> + <requirements> + <requirement type="package">yapp_env</requirement> + </requirements> + <macros> + <import>macros.xml</import> + </macros> + <version_command>echo "guppy $(guppy --version)"</version_command> + <command interpreter="bash"> + alignment-wrapper.sh ${config} + </command> + <stdio> + <expand macro="basic_errors"/> + </stdio> + <inputs> + <param name="refpkg" type="data" format="refpkg" label="Reference package"/> + <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> + </inputs> + <outputs> + <data name="aligned_seqs" format="fasta" label="Aligned sequences"/> + <data name="aligned_scores" format="txt" label="Alignment scores"/> + </outputs> + <configfiles> + <configfile name="config"> +REFPKG="${refpkg.extra_files_path}" +INPUT_SEQS="${input_seqs}" + +ALIGNED_SEQS="${aligned_seqs}" +ALIGNED_SCORES="${aligned_scores}" + </configfile> + </configfiles> + <!-- The contents of the help tag is parsed as reStructuredText. Please see + help-template.rst for examples of commonly-used sections in other Galaxy + tools. --> + <help> + +.. class:: infomark + +**What it does** + +This tool aligns query sequences with the reference sequences used to make the +reference tree contained in the reference package and then merges the query and +reference sequences. + + </help> +</tool>