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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit f971832d2b34a182314e5201ea6895dd207c5923 |
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modified:
fasta2shrep_gspan.xml |
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| diff -r 6942ec989fed -r aae41396646e fasta2shrep_gspan.xml --- a/fasta2shrep_gspan.xml Mon Feb 27 12:02:23 2017 -0500 +++ b/fasta2shrep_gspan.xml Mon Mar 13 18:02:20 2017 -0400 |
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| @@ -1,42 +1,76 @@ <tool id="gspan" name="fasta_to_gspan" version="0.1"> - <requirements> - <requirement type="package" version="0.1.9">graphclust-wrappers</requirement> - <requirement type="package" version="2.1.6">rnashapes</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ - - 'fasta2shrep_gspan.pl' --fasta '$dataFasta' $i_crop_unpaired_ends $i_abstr $i_stacks -t "3=0,5=80" -M $M -c $rel_energy_range -win $wins -shift $shift $u $seq_graph_t --group $group + <requirements> + <requirement type="package" version="0.1.10">graphclust-wrappers</requirement> + <requirement type="package" version="2.1.6">rnashapes</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + fasta2shrep_gspan.pl + --fasta '$dataFasta' + $i_crop_unpaired_ends + $i_abstr + $i_stacks + -t '3=0,5=80' + -M $M + -c $rel_energy_range + -win $wins + -shift $shift + $u + $seq_graph_t + -group $group -]]> - </command> - <inputs> - <param type="data" name="dataFasta" format="fasta" /> - <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean" label="Add stacking information to graphs." help="-stack"/> - <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/> - <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/> - <param name="M" type="integer" value="5" size="7" label="Max number of shreps that should be taken per window." help="-M"/> - <param name="rel_energy_range" type="integer" value="20" size="7" label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/> - <param name="wins" type="text" value="40,150" size="20" label=" A list of window sizes to use" help="comma separated integers"/> - <param name="shift" type="integer" value="30" size="7" label="The shift of the window, relative to the window size given inpercent." help="by default 30"/> - <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean" label="Ignore unstable structures (RNAshapes)" help="-u"/> - <param name="seq_graph_t" truevalue="--seq-graph-t" falsevalue="" checked="True" type="boolean" label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/> - <param name="group" type="integer" value="10000" size="7" label="Group size." help="by default 10000"/> - </inputs> - <outputs> - <data name="gspan.zip" format="searchgui_archive" from_work_dir="GSPAN_Outputs/1.group.gspan.bz2" label="gspan zip" /> - </outputs> - <tests> - <test> - <param name="dataFasta" value="data.fasta"/> - <output name="gspan.zip" file="GSPAN_Outputs/1.group.gspan.bz2" /> - </test> - </tests> - <help> - <![CDATA[ + ]]> + </command> + <inputs> + <param type="data" name="dataFasta" format="fasta" label="Input file in FASTA format" /> + <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean" + label="Add stacking information to graphs." help="-stack"/> + <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean" + label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/> + <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean" + label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/> + <param name="M" type="integer" value="5" label="Max number of shreps that should be taken per window." help="-M"/> + <param name="rel_energy_range" type="integer" value="20" + label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/> + <param name="wins" type="text" value="40,150" + label=" A list of window sizes to use" help="comma separated integers"/> + <param name="shift" type="integer" value="30" + label="The shift of the window, relative to the window size given inpercent." help="by default 30"/> + <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean" + label="Ignore unstable structures (RNAshapes)" help="-u"/> + <param name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="True" type="boolean" + label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/> + <param name="group" type="integer" value="10000" + label="Group size" help="by default 10000"/> + </inputs> + <outputs> + <collection name="gspan_compressed" type="list" label="GSPAN Groups" > + <discover_datasets pattern="(?P<name>.*)\.bz2$" directory="GSPAN_Outputs" /> + </collection> + </outputs> + <tests> + <test> + <param name="dataFasta" value="data.fasta"/> + <param name="i_stacks" value="True" /> + <param name="i_abstr" value="False" /> + <param name="i_crop_unpaired_ends" value="False" /> + <param name="M" value="5" /> + <param name="rel_energy_range" value="20" /> + <param name="wins" value="40,150" /> + <param name="shift" value="30" /> + <param name="u" value="True" /> + <param name="seq_graph_t" value="True" /> + <param name="group" value="10000" /> + <output_collection name="gspan_compressed" type="list"> + <element name="1.group.gspan" file="GSPAN_Outputs/1.group.gspan.bz2"/> + </output_collection> + </test> + </tests> + <help> + <![CDATA[ **What it does** @@ -84,15 +118,9 @@ + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' ]]> - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/bts224</citation> - <citation type="bibtex">@article{jan:gie:2015, -author={Janssen, Stefan and Giegerich, Robert}, -title={The RNA shapes studio}, -journal={Bioinformatics}, -year={2015}, -doi={10.1093/bioinformatics/btu649}, -url={http://bioinformatics.oxfordjournals.org/content/31/3/423.abstract}}</citation> - </citations> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts224</citation> + <citation type="doi">10.1093/bioinformatics/btu649</citation> + </citations> </tool> |