# HG changeset patch
# User bgruening
# Date 1482414017 18000
# Node ID a81b012ef352e65352fe551814a55cc3b0fc0a47
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
diff -r 000000000000 -r a81b012ef352 dir2html.py
--- /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 = ['\n']
+ for root, dirs, files in os.walk( directory ):
+ root = root.rstrip('/')
+ ret.append(' | %s |
\n' % escape( os.path.split(root)[-1] ))
+ for file in files:
+ ret.append(' | %s |
\n' % ( os.path.join( os.path.split(root)[-1], file), escape(file) ))
+ ret.append('
')
+ return ''.join(ret)
+
+def make_html( directory ):
+ return '\n'.join([''
+ '',
+ ' Search results',
+ ' ',
+ '',
+ '',
+ 'Search Results
',
+ make_table( directory ),
+ '',
+ ''])
+
+if __name__ == '__main__':
+ if len(sys.argv) == 2:
+ directory_path = sys.argv[1]
+ else: top = '.'
+ print make_html( directory_path )
+
diff -r 000000000000 -r a81b012ef352 graphclust.xml
--- /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 @@
+
+ alignment-free structural clustering of local RNA secondary structures
+
+ GraphClust
+ locarna
+ RNAShapes
+ cmfinder
+ infernal
+ rnaz
+ vienna_rna
+
+
+ $output
+]]>
+
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## OPTS_RNAfold --noLP
+
+
+
+
+
+##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
+
+
+
+
+
+
+
+
+
+
+
+##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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#OPTS_nspdk -R 3 -D 3 -gt DIRECTED
+#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 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
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/bts224
+
+