changeset 0:a81b012ef352 draft default tip

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
parents
children
files dir2html.py graphclust.xml
diffstat 2 files changed, 281 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir2html.py	Thu Dec 22 08:40:17 2016 -0500
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+import os
+import sys
+from xml.sax.saxutils import escape
+
+def make_table( directory ):
+    ret = ['<table class="fileList">\n']
+    for root, dirs, files in os.walk( directory ):
+        root = root.rstrip('/')
+        ret.append('   <tr><td class="directory">%s</td></tr>\n' % escape( os.path.split(root)[-1] ))
+        for file in files:
+            ret.append('   <tr><td class="file"><a href="%s">%s</a></td></tr>\n' % ( os.path.join( os.path.split(root)[-1], file), escape(file) ))
+    ret.append('</table>')
+    return ''.join(ret)
+
+def make_html( directory ):
+    return '\n'.join(['<html>'
+                      '<head>',
+                      '   <title>Search results</title>',
+                      '   <style type="text/css">',
+                      '      table.fileList { text-align: left; }',
+                      '      td.directory { font-weight: bold; }',
+                      '      td.file { padding-left: 4em; }',
+                      '   </style>',
+                      '</head>',
+                      '<body>',
+                      '<h1>Search Results</h1>',
+                      make_table( directory ),
+                      '</body>',
+                      '</html>'])
+                   
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        directory_path = sys.argv[1]
+    else: top = '.'
+    print make_html( directory_path )
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphclust.xml	Thu Dec 22 08:40:17 2016 -0500
@@ -0,0 +1,244 @@
+<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>