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comparison fasta2shrep_gspan.xml @ 4:aae41396646e draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 18:02:20 -0400
parents 6942ec989fed
children 8641b7be8757
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3:6942ec989fed 4:aae41396646e
1 <tool id="gspan" name="fasta_to_gspan" version="0.1"> 1 <tool id="gspan" name="fasta_to_gspan" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.9">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
4 <requirement type="package" version="2.1.6">rnashapes</requirement> 4 <requirement type="package" version="2.1.6">rnashapes</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 fasta2shrep_gspan.pl
12 --fasta '$dataFasta'
13 $i_crop_unpaired_ends
14 $i_abstr
15 $i_stacks
16 -t '3=0,5=80'
17 -M $M
18 -c $rel_energy_range
19 -win $wins
20 -shift $shift
21 $u
22 $seq_graph_t
23 -group $group
11 24
12 'fasta2shrep_gspan.pl' --fasta '$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 25 ]]>
13 26 </command>
14 ]]> 27 <inputs>
15 </command> 28 <param type="data" name="dataFasta" format="fasta" label="Input file in FASTA format" />
16 <inputs> 29 <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean"
17 <param type="data" name="dataFasta" format="fasta" /> 30 label="Add stacking information to graphs." help="-stack"/>
18 <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean" label="Add stacking information to graphs." help="-stack"/> 31 <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean"
19 <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/> 32 label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
20 <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/> 33 <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean"
21 <param name="M" type="integer" value="5" size="7" label="Max number of shreps that should be taken per window." help="-M"/> 34 label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
22 <param name="rel_energy_range" type="integer" value="20" size="7" label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/> 35 <param name="M" type="integer" value="5" label="Max number of shreps that should be taken per window." help="-M"/>
23 <param name="wins" type="text" value="40,150" size="20" label=" A list of window sizes to use" help="comma separated integers"/> 36 <param name="rel_energy_range" type="integer" value="20"
24 <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"/> 37 label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
25 <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean" label="Ignore unstable structures (RNAshapes)" help="-u"/> 38 <param name="wins" type="text" value="40,150"
26 <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"/> 39 label=" A list of window sizes to use" help="comma separated integers"/>
27 <param name="group" type="integer" value="10000" size="7" label="Group size." help="by default 10000"/> 40 <param name="shift" type="integer" value="30"
28 </inputs> 41 label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
29 <outputs> 42 <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean"
30 <data name="gspan.zip" format="searchgui_archive" from_work_dir="GSPAN_Outputs/1.group.gspan.bz2" label="gspan zip" /> 43 label="Ignore unstable structures (RNAshapes)" help="-u"/>
31 </outputs> 44 <param name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="True" type="boolean"
32 <tests> 45 label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
33 <test> 46 <param name="group" type="integer" value="10000"
34 <param name="dataFasta" value="data.fasta"/> 47 label="Group size" help="by default 10000"/>
35 <output name="gspan.zip" file="GSPAN_Outputs/1.group.gspan.bz2" /> 48 </inputs>
36 </test> 49 <outputs>
37 </tests> 50 <collection name="gspan_compressed" type="list" label="GSPAN Groups" >
38 <help> 51 <discover_datasets pattern="(?P&lt;name&gt;.*)\.bz2$" directory="GSPAN_Outputs" />
39 <![CDATA[ 52 </collection>
53 </outputs>
54 <tests>
55 <test>
56 <param name="dataFasta" value="data.fasta"/>
57 <param name="i_stacks" value="True" />
58 <param name="i_abstr" value="False" />
59 <param name="i_crop_unpaired_ends" value="False" />
60 <param name="M" value="5" />
61 <param name="rel_energy_range" value="20" />
62 <param name="wins" value="40,150" />
63 <param name="shift" value="30" />
64 <param name="u" value="True" />
65 <param name="seq_graph_t" value="True" />
66 <param name="group" value="10000" />
67 <output_collection name="gspan_compressed" type="list">
68 <element name="1.group.gspan" file="GSPAN_Outputs/1.group.gspan.bz2"/>
69 </output_collection>
70 </test>
71 </tests>
72 <help>
73 <![CDATA[
40 74
41 **What it does** 75 **What it does**
42 76
43 For each fragment of input sequence we use RNAshapes to create a set of structures. 77 For each fragment of input sequence we use RNAshapes to create a set of structures.
44 The default parameters for example consider for each input fragment again a 78 The default parameters for example consider for each input fragment again a
82 + **seq-graph-t** : Add for each 't #' a graph which contains no structure 116 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
83 117
84 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' 118 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
85 119
86 ]]> 120 ]]>
87 </help> 121 </help>
88 <citations> 122 <citations>
89 <citation type="doi">10.1093/bioinformatics/bts224</citation> 123 <citation type="doi">10.1093/bioinformatics/bts224</citation>
90 <citation type="bibtex">@article{jan:gie:2015, 124 <citation type="doi">10.1093/bioinformatics/btu649</citation>
91 author={Janssen, Stefan and Giegerich, Robert}, 125 </citations>
92 title={The RNA shapes studio},
93 journal={Bioinformatics},
94 year={2015},
95 doi={10.1093/bioinformatics/btu649},
96 url={http://bioinformatics.oxfordjournals.org/content/31/3/423.abstract}}</citation>
97 </citations>
98 </tool> 126 </tool>