Mercurial > repos > bgruening > graphclust
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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--- /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>