Mercurial > repos > rnateam > blockclust

comparison blockclust.xml @ 0:768a67f6ae18 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rnateam
date Tue, 06 May 2014 07:49:25 -0400
parents
children a92d8689aa30
comparison
equal deleted inserted replaced
-1:000000000000 0:768a67f6ae18
1 <tool id="blockclust" name="BlockClust" version="1.0.0">
2 <description>Non-coding RNA clustering from deep sequencing read profiles</description>
3 <requirements>
4 <requirement type="package" version="1.0">blockclust</requirement>
5 <requirement type="package" version="1.1">eden</requirement>
6 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement>
8 <requirement type="package" version="12.135">mcl</requirement>
9 <requirement type="package" version="1.0">blockclust_rlibs</requirement>
10 </requirements>
11 <version_command>echo '1.0'</version_command>
12 <command>
13
14 #if str($tool_mode.operation) == "pre":
15 #set $outputdir = $tags_bed.extra_files_path
16 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
17 #elif str($tool_mode.operation) == "clust":
18 #set $outputdir = $clusters.extra_files_path
19 #set $accept_bed=list()
20 #set $reject_bed=list()
21 ## prepare annotations
22 #if str($tool_mode.reference) == "hg19":
23 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
24 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
25 #elif str($tool_mode.reference) == "mm10":
26 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
27 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
28 #elif str($tool_mode.reference) == "dm3":
29 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
30 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
31 #elif str($tool_mode.reference) == "rheMac3":
32 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
33 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
34 #elif str($tool_mode.reference) == "panTro4":
35 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
36 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
37 #elif str($tool_mode.reference) == "xenTro3":
38 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
39 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
40 #elif str($tool_mode.reference) == "celWS235":
41 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
42 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
43 #elif str($tool_mode.reference) == "tair10":
44 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
45 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
46 #end if
47 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
48 -t $tool_mode.input_bbo
49 -a #echo ''.join( $accept_bed )
50 -r #echo ''.join( $reject_bed )
51 -o $outputdir
52 #if str($tool_mode.pred.enable_pred) == "yes":
53 -p
54 -pm $tool_mode.pred.pred_mode
55 -md \$BLOCKCLUST_DATA_PATH/models
56 -x 3;
57 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
58 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
59 #elif str($tool_mode.pred.pred_mode) == "model_based":
60 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
61 #end if
62 #else:
63 ;
64 #end if
65
66 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
67 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
68 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
69 #elif str($tool_mode.operation) == "post":
70 #set $outputdir = $clusters_bed.extra_files_path
71 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
72 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
73 cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust
74 #end if
75 </command>
76 <inputs>
77 <conditional name="tool_mode">
78 <param name="operation" type="select" label="Select mode of operation">
79 <option value="pre">Pre-processing </option>
80 <option value="clust">Clustering</option>
81 <option value="post">Post-processing</option>
82 </param>
83 <when value="pre">
84 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
85 </when>
86 <when value="clust">
87 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
88 <param name="reference" type="select" label="Select reference genome">
89 <option value="hg19">Human (hg19)</option>
90 <option value="mm10">Mouse (mm10)</option>
91 <option value="dm3">Fly (dm3)</option>
92 <option value="rheMac3">Monkey (rheMac3)</option>
93 <option value="panTro4">Chimp (panTro4)</option>
94 <option value="xenTro3">Frog (xenTro3)</option>
95 <option value="celWS235">C. elegans (celWS235)</option>
96 <option value="tair10">Arabidopsis thaliana (tair10)</option>
97 </param>
98 <conditional name="pred">
99 <param name="enable_pred" type="select" label="Would you like to perform classification?">
100 <option value="no">No</option>
101 <option value="yes">Yes</option>
102 </param>
103 <when value="yes">
104 <param name="pred_mode" type="select" label="Mode of classification">
105 <option value="model_based">Model based</option>
106 <option value="nearest_neighbour">Nearest neighbour</option>
107 </param>
108 </when>
109 </conditional>
110 </when>
111 <when value="post">
112 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
113 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
114 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
115 </when>
116 </conditional>
117 </inputs>
118
119 <outputs>
120 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
121 <filter> tool_mode["operation"]=="pre"</filter>
122 </data>
123 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
124 <filter> tool_mode["operation"]=="clust"</filter>
125 </data>
126 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
127 <filter> tool_mode["operation"]=="clust"</filter>
128 </data>
129 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}">
130 <filter>
131 ((
132 tool_mode["operation"] == 'clust' and
133 tool_mode["pred"]["enable_pred"] == "yes" and
134 tool_mode["pred"]["pred_mode"] == "model_based"
135 ))
136 </filter>
137 </data>
138 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}">
139 <filter>
140 ((
141 tool_mode["operation"] == 'clust' and
142 tool_mode["pred"]["enable_pred"] == "yes" and
143 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
144 ))
145 </filter>
146 </data>
147 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
148 <filter> tool_mode["operation"]=="clust"</filter>
149 </data>
150 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
151 <filter> tool_mode["operation"]=="post"</filter>
152 </data>
153 <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
154 <filter> tool_mode["operation"]=="post"</filter>
155 </data>
156 </outputs>
157 <help>
158
159 .. class:: infomark
160
161 **What it does**
162
163 Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.
164
165 **Inputs**
166
167 BlockClust needs output of tool blockbuster as input
168
169 **Output**
170
171 BlockClust produces a fasta file containing clusters.
172
173 ------
174
175 **Licenses**
176
177 If **BlockClust** is used to obtain results for scientific publications it
178 should be cited as [1]_.
179
180 **References**
181
182 .. [1]
183
184
185 </help>
186 </tool>