Mercurial > repos > jdv > b2b_summarize_assembly
view summarize_assembly.xml @ 1:5def63878840 draft default tip
"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author | jdv |
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date | Tue, 28 Sep 2021 06:16:07 +0000 |
parents | 114353d77370 |
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<tool id="b2b_summarize_assembly" name="Summarize assembly" version="0.02"> <description>Calculate and print basic assembly summary stats</description> <!-- ***************************************************************** --> <requirements> <!-- <requirement type="package" version="0.003">b2b-utils</requirement> --> <requirement type="package" version="0.008002">perl-biox-seq</requirement> <requirement type="package">perl-list-moreutils</requirement> </requirements> <!-- ***************************************************************** --> <version_command>perl $__tool_directory__/summarize_assembly --version | perl -wnE'print "$1\n" for /summarize_assembly v(.+)/g'</version_command> <!-- ***************************************************************** --> <command detect_errors="aggressive"> <![CDATA[ perl $__tool_directory__/summarize_assembly --fasta $input1 --cutoffs $cutoffs #if $split_N: --split_N #end if #if $strip_N: --strip_N #end if > $report ; ]]> </command> <!-- ***************************************************************** --> <inputs> <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" /> <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)"> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=" " /></valid> </sanitizer> </param> <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" /> <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" /> </inputs> <!-- ***************************************************************** --> <outputs> <data format="txt" name="report" label="${tool.name} on ${on_string}" /> </outputs> <!-- ***************************************************************** --> <tests> <test> <param name="input1" value="assembly.fa" ftype="fasta" /> <param name="cutoffs" value="50 90 95" /> <output name="report" file="summarize.txt" compare="diff" /> </test> <test> <param name="input1" value="assembly.fa" ftype="fasta" /> <param name="cutoffs" value="50 90 95" /> <param name="strip_N" value="True" /> <output name="report" file="summarize.strip.txt" compare="diff" /> </test> <test> <param name="input1" value="assembly.fa" ftype="fasta" /> <param name="cutoffs" value="50 90 95" /> <param name="split_N" value="True" /> <output name="report" file="summarize.split.txt" compare="diff" /> </test> </tests> <!-- ***************************************************************** --> <help> summarize_assembly is a utility from b2b-utils. It takes a FASTA file and optionally a list of cutoff values as input and prints out summary information about the contigs/scaffolds contained in the file. You can, of course, supply a FASTA file of any sort of nucleic acid sequences, but the summary information makes most sense for contigs from genomic sequencing assemblies. </help> <!-- ***************************************************************** --> <citations> </citations> </tool>