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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
author bgruening
date Thu, 22 Dec 2016 08:40:17 -0500
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<tool id="graphclust" name="graphclust" version="0.1">
    <description>alignment-free structural clustering of local RNA secondary structures</description>
    <requirements>
        <requirement type="package">GraphClust</requirement>
        <requirement type="package">locarna</requirement>
        <requirement type="package">RNAShapes</requirement>
        <requirement type="package">cmfinder</requirement>
        <requirement type="package">infernal</requirement>
        <requirement type="package">rnaz</requirement>
        <requirement type="package">vienna_rna</requirement>
    </requirements>
    <command>
<![CDATA[
        MASTER_GraphClust.pl
            --fasta $input_fasta
            --config $graphclust_config
            --root $output.files_path
            --threads "\${GALAXY_SLOTS:-12}";

        python dir2html.py $output.files_path/RESULTS > $output
]]>
    </command>
    <configfiles>
        <configfile name="graphclust_config">
            GLOBAL_group_size   $GLOBAL_group_size
            GLOBAL_hit_blacklist_overlap    $GLOBAL_hit_blacklist_overlap
            GLOBAL_iterations   $GLOBAL_iterations
            GLOBAL_num_clusters     $GLOBAL_num_clusters
            GLOBAL_plfold_minlen    $GLOBAL_plfold_minlen

            OPTS_RNAfold    --noLP
            OPTS_RNAplfold  --noLP -c  $RNAplfold_c  -L  $RNAplfold_L  -W  $RNAplfold_W
            OPTS_fasta2shrep_gspan  -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph
            OPTS_locarna_maligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
            OPTS_locarna_model  -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
            OPTS_locarna_p_model  -p $locarna_p --max-diff-am $locarna_max_diff_am --tau 100 --max-diff $locarna_max_diff --struct-weight $locarna_struct_weight --plfold-span 150 --plfold-winsize 200 --temperature $locarna_temperature --mea-beta 400 --consistency-transformation
            OPTS_locarna_paligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --indel-open $locarna_indel_open --indel $locarna_indel --struct-weight $locarna_struct_weight
            OPTS_nspdk  -R $nspdk_R -D $nspdk_R -gt $nspdk_gt
            OPTS_nspdk_centers  -ensf 5 -oc -usn

            center_model_type   5
            center_subtree_max  7
            center_subtree_min  3
            center_tree_aligs   2
            center_tree_type    3
            cm_bitscore_sig 1
            cm_calibrate    0
            cm_max_eval 0.001
            cm_min_bitscore 15
            cm_top_only 0
            evaluate    0
            evaluate_class0_as_fp   0
            evaluate_min_overlap    0.51
            input_add_revcompl  0
            input_blastclust    1
            input_blastclust_id 90
            input_blastclust_len    0.90
            input_seq_min_length    $other_input_seq_min_length
            input_win_shift $other_input_win_shift
            input_win_size  0
            nspdk_fcs   1
            nspdk_greylist_num  0
            nspdk_knn_center    10
            nspdk_nhf   500
            nspdk_nhf_max   1000
            nspdk_nhf_step  50
            results_merge_cluster_ol    0.66
            results_merge_overlap   0.51
            results_min_cluster_size    $other_results_min_cluster_size
            results_partition_type  soft
            results_top_num 10
        </configfile>
    </configfiles>
    <inputs>

        <param name="input_fasta" type="data" format="fasta" label="Fasta file containing sequeces you want to cluster" />

<!--
        <conditional name="OPTS_GLOBAL">
            <param name="OPTS_GLOBAL_selector" type="select" label="Global advanced options">
                <option value="basic" selected="True">Hide Advanced Options</option>
                <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
-->
                <param name="GLOBAL_group_size" type="integer" value="50" label="GLOBAL_group_size" />
                <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" label="GLOBAL_hit_blacklist_overlap" />
                <param name="GLOBAL_iterations" type="integer" value="5" label="GLOBAL_iterations" />
                <param name="GLOBAL_num_clusters" type="integer" value="3" label="GLOBAL_num_clusters" />
                <param name="GLOBAL_plfold_minlen" type="integer" value="150" label="GLOBAL_plfold_minlen" />
<!--
            </when>
        </conditional>
-->

##        OPTS_RNAfold                  --noLP
<!--
        <conditional name="OPTS_RNAplfold">
            <param name="OPTS_RNAplfold_selector" type="select" label="RNAplfold advanced options">
                <option value="basic" selected="True">Hide Advanced Options</option>
                <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
-->
                <param name="RNAplfold_c" type="float" value="0.0005" label="Report only base pairs with an average probability greater than this value in the dot plot" />
                <param name="RNAplfold_L" type="integer" value="200" label="Set the maximum allowed separation of a base pair to span" />
                <param name="RNAplfold_W" type="integer" value="300" label="Average the pair probabilities over windows of given size" />
<!--
            </when>
        </conditional>
-->
##OPTS_RNAplfold                --noLP

##OPTS_fasta2shrep_gspan        -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph

<!--
        <conditional name="OPTS_locarna">
            <param name="OPTS_locarna_selector" type="select" label="LocaRNA advanced options">
                <option value="basic" selected="True">Hide Advanced Options</option>
                <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
-->
                <param name="locarna_p" type="float" value="0.001" label="Minimal probability" />
                <param name="locarna_max_diff_am" type="integer" value="50" label="Maximal difference for sizes of matched arcs" />
                <param name="locarna_tau" type="integer" value="50" label="Tau factor in percent" />
                <param name="locarna_max_diff" type="integer" value="100" label="Maximal difference for alignment traces" />
                <param name="locarna_struct_weight" type="integer" value="180" label="Maximal weight of 1/2 arc match" />
                <param name="locarna_temperature" type="integer" value="180" label="Temperature for PF-computation" />
                <param name="locarna_indel_open" type="integer" value="-400" label="Indel opening score" />
                <param name="locarna_indel" type="integer" value="-200" label="Indel score" />
<!--
            </when>
        </conditional>
-->
##OPTS_locarna_maligs           -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
##OPTS_locarna_model            -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
##OPTS_locarna_p_model          -p 0.001 --max-diff-am 50 --tau 100 --max-diff 100 --struct-weight 180 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation
##OPTS_locarna_paligs           -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --indel-open -400 --indel -200 --struct-weight 180

<!--
        <conditional name="OPTS_nspdk">
            <param name="OPTS_nspdk_selector" type="select" label="NSPDK advanced options">
                <option value="basic" selected="True">Hide Advanced Options</option>
                <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
-->
                <param name="nspdk_R" type="integer" value="3" label="Radius" />
                <param name="nspdk_D" type="integer" value="3" label="Distance" />
                <param name="nspdk_gt" type="select" label="graph type" >
                    <option value="DIRECTED" selected="True">DIRECTED</option>
                    <option value="UNDIRECTED">UNDIRECTED</option>
                </param>
                <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
                <param name="nspdk_knn_center" type="integer" value="10" label="number of nearest neighbors" />
                <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
                <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
                <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
<!--
            </when>
        </conditional>
-->
#OPTS_nspdk                    -R 3 -D 3 -gt DIRECTED
#OPTS_nspdk_centers            -ensf 5 -oc -usn

<!--
        <conditional name="OPTS_other">
            <param name="OPTS_other_selector" type="select" label="Other advanced options">
                <option value="basic" selected="True">Hide Advanced Options</option>
                <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
-->
                <param name="other_input_seq_min_length" type="integer" value="50" label="input_seq_min_length" />
                <param name="other_input_win_shift" type="integer" value="33" label="input_win_shift" />
                <param name="other_results_min_cluster_size" type="integer" value="5" label="results_min_cluster_size" />
<!--
            </when>
        </conditional>
-->
##center_model_type             5
##center_subtree_max            7
##center_subtree_min            3
##center_tree_aligs             2
##center_tree_type              3
##cm_bitscore_sig               1
##cm_calibrate                  0
##cm_max_eval                   0.001
##cm_min_bitscore               15
##cm_top_only                   0
##evaluate                      0
##evaluate_class0_as_fp         0
##evaluate_min_overlap          0.51
##input_add_revcompl            0
##input_blastclust              1
##input_blastclust_id           90
##input_blastclust_len          0.90
##input_seq_min_length          50
##input_win_shift               33
##input_win_size                0
##nspdk_fcs                     1
##nspdk_greylist_num            0
##nspdk_knn_center              10
##nspdk_nhf                     500
##nspdk_nhf_max                 1000
##nspdk_nhf_step                50
##results_merge_cluster_ol      0.66
##results_merge_overlap         0.51
##results_min_cluster_size      5
##results_partition_type        soft
##results_top_num               10

    </inputs>
    <outputs>
        <data name="output" format="html" label="GraphClust on ${on_string}"/>
    </outputs>
    <help>
<![CDATA[

.. class:: infomark

**What it does**

GraphClust

TODO

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/bts224</citation>
    </citations>
</tool>