Mercurial > repos > bgruening > hicexplorer_hicfindrestrictionsites
diff hicFindRestrictionSites.xml @ 6:8823a9d45ed0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
---|---|
date | Tue, 16 Mar 2021 14:51:57 +0000 |
parents | 3c03ddb45833 |
children | 9369e9b11b8d |
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--- a/hicFindRestrictionSites.xml Fri Dec 11 21:44:35 2020 +0000 +++ b/hicFindRestrictionSites.xml Tue Mar 16 14:51:57 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>identify restriction enzyme sites</description> <macros> <token name="@BINARY@">hicFindRestSite</token> @@ -11,31 +11,25 @@ --searchPattern '$searchPattern' --outFile restriction_site.bed - ]]></command> + ]]> </command> <inputs> - <param argument="--fasta" type="data" format='fasta' - label="Fasta file for the organism genome." - help="The organism genome fasta file to compute the restriction enzyme position."/> - <param argument="--searchPattern" type="text" value="" - label="Restriction enzyme sequence" - help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\". + <param argument="--fasta" type="data" format='fasta,fasta.gz' label="Fasta file for the organism genome." help="The organism genome fasta file to compute the restriction enzyme position." /> + <param argument="--searchPattern" type="text" value="" label="Restriction enzyme sequence" help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\". Both, forward and reverse strand are searched for a match. The pattern is a regexp and can contain regexp specif syntax (see https://docs.python.org/2/library/re.html). For example the pattern - CG..GC will find all occurrence of CG followed by any two bases and then GC.'/> + CG..GC will find all occurrence of CG followed by any two bases and then GC.'> + <validator type="expression" message="Only ASCII characters are allowed.">value.isascii()</validator> + </param> </inputs> <outputs> - - <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites"/> - + <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites" /> </outputs> <tests> <test> - <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta"/> - - <param name="searchPattern" value="GTAC"/> - - <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" compare="sim_size"/> + <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta" /> + <param name="searchPattern" value="GTAC" /> + <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" /> </test> </tests> <help><![CDATA[ @@ -49,6 +43,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>