Mercurial > repos > rnateam > locarna_reliability_profile
diff macros.xml @ 0:7dd1f41aee4d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author | rnateam |
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date | Wed, 28 Dec 2016 18:52:45 -0500 |
parents | |
children | 9942e1b7646c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 28 18:52:45 2016 -0500 @@ -0,0 +1,178 @@ +<macros> + <token name="@VERSION@">1.9.0</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">locarna</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + + <xml name="version"> + <version_command> + <![CDATA[ + mlocarna --version + ]]> + </version_command> + </xml> + + <xml name="bed_anchors"> + <conditional name="bed_anchors"> + <param name="bed_anchors_selector" type="select" label="Anchor constraints" + help="Anchor constraints in bed format specify positions of + named anchor regions per sequence. The sequence names + ('contig' names have to correspond to the fasta input + sequence names. Anchor names must be unique per sequence + and regions of the same name for different sequences + must have the same length. This constrains the alignment + to align all regions of the same name."> + <option value="no">Don't load anchor constraints from bed file</option> + <option value="yes">Load anchor constraints from bed file</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="bed_anchors_file" type="data" format="tabular" + label="Anchor constraint specification in bed format" + /> + </when> + </conditional> + </xml> + + <xml name="common_scoring_parameters"> + <param name="struct_weight" argument="struct-weight" + label="Structure weight" type="integer" + value="200" min="0" max="800" /> + <param name="indel_opening" argument="indel-opening" + label="Indel opening score" type="integer" + value="-500" max="0" min="-1500" /> + <param argument="indel" label="Indel score" type="integer" + value="-350" min="-1000" max="0" /> + <param argument="tau" type="integer" value="50" + min="0" max="200" + label="Sequence contribution at structure match in percent"/> + + <conditional name="sequence_score"> + <param name="sequence_score_selector" type="select" label="Type of sequence score contribution"> + <option value="ribofit">Use ribofit</option> + <option value="ribosum">Use RIBOSUM85_60</option> + <option value="match">Simple match/mismatch costs</option> + </param> + <when value="ribofit" /> + <when value="ribosum" /> + <when value="match"> + <param name="match" type="integer" value="50" + min="0" max="400" + label="Match score" /> + <param name="mismatch" type="integer" value="0" + min="-400" max="0" + label="Mismatch score" /> + </when> + </conditional> + </xml> + + <xml name="plfolding_parameters"> + <param name="plfold_span" argument="--plfold-span" + type="integer" value="150" min="-1" max="400" + label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" /> + + <param name="plfold_winsize" argument="--plfold-winsize" + type="integer" value="300" min="-1" max="800" + label="Window size for local folding" /> + </xml> + + <xml name="common_folding_parameters"> + <param name="rnafold_temperature" argument="rnafold-temperature" + type="float" value="37.0" min="10" max="50" + label="Temperature for RNAfold (RNAfold's -T option)" /> + </xml> + + <xml name="common_heuristic_parameters"> + <param name="min_prob" argument="min-prob" type="float" value="0.0005" + min="0.0" max="0.2" + label="Minimal / cutoff probability" /> + + <param name="max_diff_am" argument="max-diff-am" + type="integer" value="30" + min="-1" max="300" + label="Maximal difference for sizes of matched arcs (-1=off)" /> + + <param name="max_diff" argument="max-diff" type="integer" + value="60" min="-1" max="300" + label="Maximal difference for alignment traces (-1=off)" /> + + <param name="max_diff_at_am" argument="max-diff-am" type="integer" + value="-1" min="-1" max="300" + label="Maximal difference for alignment traces, only at arc match positions" /> + + <param name="max_bps_length_ratio" argument="max-bps-length-ratio" + type="float" value="0.0" min="0.0" max="1.0" + label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> + </xml> + + <xml name="alifold_consensus_parameter"> + <param name="alifold_consensus_dp" argument="alifold-consensus-dp" + type="boolean" checked="false" + truevalue="--alifold-consensus-dp" falsevalue="" + label="Compute consensus dot plot by alifold" /> + </xml> + + <xml name="constraints"> + <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" + checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> + <param name="maxBPspan" argument="--maxBPspan" + type="integer" value="-1" min="-1" max="400" + label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> + <param name="ignore_constraints" argument="ignore-constraints" + type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" + help="Ignore all anchor and structure constraints given + in the fasta(-ish) input." /> + </xml> + + <xml name="common_other_parameters"> + </xml> + + <xml name="common_outputs"> + <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> + <filter>stdout_verbosity != '--quiet'</filter> + </data> + <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" + label="${tool.name} alignment (annotated clustal) on ${on_string}"> + <filter>'clustal' in outputs</filter> + </data> + <data format="clustal" name="clustal_strict" + from_work_dir="mlocarna_results/results/result.strict-aln" + label="${tool.name} alignment (clustal) on ${on_string}"> + <filter>'clustal_strict' in outputs</filter> + </data> + <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk" + label="${tool.name} alignment (stockholm) on ${on_string}"> + <filter>'stockholm' in outputs</filter> + </data> + <data format="txt" name="pp" + from_work_dir="mlocarna_results/results/result.pp" + label="${tool.name} alignment (PP 2.0) on ${on_string}"> + <filter>'pp' in outputs</filter> + </data> + <data format="tar.gz" name="mlocarna_results_tgz" + label="${tool.name} results archive on ${on_string}"> + <filter>'mlocarna_results' in outputs</filter> + </data> + </xml> + + <xml name="citations"> + <citations> + <citation + type="doi">10.1371/journal.pcbi.0030065</citation> + <citation type="doi">10.1261/rna.029041.111</citation> + </citations> + </xml> + + + +</macros> +