Mercurial > repos > rnateam > blockclust

comparison blockclust.xml @ 12:aab6cf87b40a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 8a847f019b21abaf4de2612dead57163b2c92d81
author rnateam
date Mon, 19 Nov 2018 08:10:14 -0500
parents 6ecd674b5b62
children dbb6ee3179bc
comparison
equal deleted inserted replaced
11:6ecd674b5b62 12:aab6cf87b40a
1 <tool id="blockclust" name="BlockClust" version="1.0.0"> 1 <tool id="blockclust" name="BlockClust" version="1.1.0">
2 <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description> 2 <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0">blockclust</requirement> 4 <requirement type="package" version="1.1.0">blockclust</requirement>
5 <requirement type="package" version="1.1">eden</requirement>
6 <requirement type="package" version="3.0.3">R</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> 5 </requirements>
11 <version_command>echo '1.0'</version_command> 6 <version_command>blockclust.py -v</version_command>
12 <command> 7 <command detect_errors="aggressive"><![CDATA[
13 <![CDATA[ 8 export BLOCKCLUST_DATA_PATH=\$(dirname \$(which blockclust.py))/../share/blockclust_data &&
9
14 #if str($tool_mode.operation) == "pre": 10 #if str($tool_mode.operation) == "pre":
15 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed 11 ln -s '$tool_mode.reads_bam' reads.bam &&
16 #elif str($tool_mode.operation) == "clust": 12 ln -f -s '${$tool_mode.reads_bam.metadata.bam_index}' reads.bam.bai &&
13 blockclust.py
14 -m PRE -bam reads.bam
15 -tbed '$tags_bed'
16 #elif str($tool_mode.operation) == "analysis":
17 #set $outputdir = $clusters.files_path 17 #set $outputdir = $clusters.files_path
18 #set $accept_bed=list() 18 blockclust.py
19 #set $reject_bed=list() 19 -o ./
20 ## prepare annotations 20 -m ANALYSIS
21 #if str($tool_mode.reference) == "hg19": 21 -f "\$BLOCKCLUST_DATA_PATH/blockclust.config"
22 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
23 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
24 #elif str($tool_mode.reference) == "mm10":
25 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
26 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
27 #elif str($tool_mode.reference) == "dm3":
28 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
29 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
30 #elif str($tool_mode.reference) == "rheMac3":
31 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
32 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
33 #elif str($tool_mode.reference) == "panTro4":
34 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
35 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
36 #elif str($tool_mode.reference) == "xenTro3":
37 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
38 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
39 #elif str($tool_mode.reference) == "celWS235":
40 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
41 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
42 #elif str($tool_mode.reference) == "tair10":
43 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
44 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
45 #end if
46 BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config
47 -t $tool_mode.input_bbo 22 -t $tool_mode.input_bbo
48 -a #echo ''.join( $accept_bed ) 23 -a "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.accept.bed"
49 -r #echo ''.join( $reject_bed ) 24 -r "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.reject.bed"
50 -o $outputdir
51 #if $tool_mode.nochr: 25 #if $tool_mode.nochr:
52 -nochr 26 -nochr
53 #end if 27 #end if
54 #if str($tool_mode.pred.enable_pred) == "yes": 28 #if str($tool_mode.pred.enable_pred) == "yes":
55 -p 29 -c
56 -pm $tool_mode.pred.pred_mode 30 -cm $tool_mode.pred.pred_mode
57 -md \$BLOCKCLUST_DATA_PATH/models; 31 -md "\$BLOCKCLUST_DATA_PATH/models"
58 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
59 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
60 #elif str($tool_mode.pred.pred_mode) == "model_based":
61 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
62 #end if
63 #else:
64 ;
65 #end if 32 #end if
66
67 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
68 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
69 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
70 #elif str($tool_mode.operation) == "post": 33 #elif str($tool_mode.operation) == "post":
71 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./; 34 blockclust.py
35 -m POST
36 -cbed '$tool_mode.clusters_bed'
37 -cs '$tool_mode.cmsearch_out'
38 -tab '$tool_mode.sim_tab_in'
39 -rfam "\$BLOCKCLUST_DATA_PATH/rfam_map.txt"
40 -o ./
72 #end if 41 #end if
73 ]]> 42 ]]>
74 </command> 43 </command>
75 <inputs> 44 <inputs>
76 <conditional name="tool_mode"> 45 <conditional name="tool_mode">
77 <param name="operation" type="select" label="Select mode of operation"> 46 <param name="operation" type="select" label="Select mode of operation">
78 <option value="pre">Pre-processing </option> 47 <option value="pre">Pre-processing </option>
79 <option value="clust">Clustering and classification</option> 48 <option value="analysis">Clustering and classification</option>
80 <option value="post">Post-processing</option> 49 <option value="post">Post-processing</option>
81 </param> 50 </param>
82 <when value="pre"> 51 <when value="pre">
83 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" /> 52 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
84 </when> 53 </when>
85 <when value="clust"> 54 <when value="analysis">
86 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" /> 55 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
87 <param name="reference" type="select" label="Select reference genome"> 56 <param name="reference" type="select" label="Select reference genome">
88 <option value="hg19">Human (hg19)</option> 57 <option value="hg19">Human (hg19)</option>
89 <option value="mm10">Mouse (mm10)</option> 58 <option value="mm10">Mouse (mm10)</option>
90 <option value="dm3">Fly (dm3)</option> 59 <option value="dm3">Fly (dm3)</option>
100 <option value="no">No</option> 69 <option value="no">No</option>
101 <option value="yes">Yes</option> 70 <option value="yes">Yes</option>
102 </param> 71 </param>
103 <when value="yes"> 72 <when value="yes">
104 <param name="pred_mode" type="select" label="Mode of classification"> 73 <param name="pred_mode" type="select" label="Mode of classification">
105 <option value="model_based">Model based</option> 74 <option value="MODEL">Model based</option>
106 <option value="nearest_neighbour">Nearest neighbour</option> 75 <option value="NEAREST">Nearest neighbour</option>
107 </param> 76 </param>
108 </when> 77 </when>
109 </conditional> 78 </conditional>
110 </when> 79 </when>
111 <when value="post"> 80 <when value="post">
116 </conditional> 85 </conditional>
117 </inputs> 86 </inputs>
118 87
119 <outputs> 88 <outputs>
120 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> 89 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
121 <filter> tool_mode["operation"]=="pre"</filter> 90 <filter>tool_mode["operation"]=="pre"</filter>
122 </data> 91 </data>
123 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > 92 <data format="pdf" name="hclust_plot" from_work_dir="hclust_tree.pdf" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
124 <filter> tool_mode["operation"]=="clust"</filter> 93 <filter>tool_mode["operation"]=="analysis"</filter>
125 </data> 94 </data>
126 <data format="bed" name="clusters" label="BlockClust: BED of predicted clusters on ${on_string}"> 95 <data format="bed" name="clusters" from_work_dir="mcl_clusters/all_clusters.bed" label="BlockClust: BED of predicted clusters on ${on_string}">
127 <filter> tool_mode["operation"]=="clust"</filter> 96 <filter>tool_mode["operation"]=="analysis"</filter>
128 </data> 97 </data>
129 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}"> 98 <data format="bed" name="model_based_pred_bed" from_work_dir="model_based_predictions.txt" label="BlockClust: Model based predictions BED on ${on_string}">
130 <filter> 99 <filter>
131 (( 100 ((
132 tool_mode["operation"] == 'clust' and 101 tool_mode["operation"] == 'analysis' and
133 tool_mode["pred"]["enable_pred"] == "yes" and 102 tool_mode["pred"]["enable_pred"] == "yes" and
134 tool_mode["pred"]["pred_mode"] == "model_based" 103 tool_mode["pred"]["pred_mode"] == "MODEL"
135 )) 104 ))
136 </filter> 105 </filter>
137 </data> 106 </data>
138 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> 107 <data format="bed" name="nearest_neighbour_pred_bed" from_work_dir="nearest_neighbour_predictions.txt" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
139 <filter> 108 <filter>
140 (( 109 ((
141 tool_mode["operation"] == 'clust' and 110 tool_mode["operation"] == 'analysis' and
142 tool_mode["pred"]["enable_pred"] == "yes" and 111 tool_mode["pred"]["enable_pred"] == "yes" and
143 tool_mode["pred"]["pred_mode"] == "nearest_neighbour" 112 tool_mode["pred"]["pred_mode"] == "NEAREST"
144 )) 113 ))
145 </filter> 114 </filter>
146 </data> 115 </data>
147 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> 116 <data format="tabular" name="sim_tab_out" from_work_dir="discretized.gspan.tab" label="BlockClust: Pairwise similarities on ${on_string}">
148 <filter> tool_mode["operation"]=="clust"</filter> 117 <filter>tool_mode["operation"]=="analysis"</filter>
149 </data> 118 </data>
150 <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" > 119 <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >
151 <filter> tool_mode["operation"]=="post"</filter> 120 <filter>tool_mode["operation"]=="post"</filter>
152 </data> 121 </data>
153 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > 122 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
154 <filter> tool_mode["operation"]=="post"</filter> 123 <filter>tool_mode["operation"]=="post"</filter>
155 </data> 124 </data>
156 </outputs> 125 </outputs>
126 <tests>
127 <!-- Test: PRE mode -->
128
129 <test expect_num_outputs="1">
130 <param name="operation" value="pre"/>
131 <param name="reads_bam" value="test.bam"/>
132 <output name="tags_bed">
133 <assert_contents>
134 <has_text_matching expression="chr6\t26555497\t26555527\ttag_10|1|19\t0.052632\t+" />
135 <has_text_matching expression="chr11\t122017275\t122017297\ttag_30|1|3\t0.333333\t-" />
136 </assert_contents>
137 </output>
138 </test>
139
140 <!-- Test: Clustering only -->
141 <test expect_num_outputs="3">
142 <param name="operation" value="analysis"/>
143 <param name="input_bbo" value="test.tabular"/>
144 <param name="reference" value="hg19"/>
145 <param name="enable_pred" value="no"/>
146 <output name="clusters">
147 <assert_contents>
148 <has_text_matching expression="chr1\t173833959\t173834043\t10:snoRNA_CD-box:blockgroup_939:cluster_1\t451.50\t-" />
149 <has_text_matching expression="chr13\t92003008\t92003075\t8:miRNA:blockgroup_256:cluster_3\t2950.50\t\+" />
150 </assert_contents>
151 </output>
152 </test>
153
154 <!-- Test: Model based prediction -->
155
156 <test expect_num_outputs="4">
157 <param name="operation" value="analysis"/>
158 <param name="input_bbo" value="test.tabular"/>
159 <param name="reference" value="hg19"/>
160 <param name="enable_pred" value="yes"/>
161 <param name="pred_mode" value="MODEL"/>
162 <output name="model_based_pred_bed">
163 <assert_contents>
164 <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" />
165 </assert_contents>
166 </output>
167 </test>
168
169 <!-- Test: Nearest neighbour based prediction -->
170
171 <test expect_num_outputs="4">
172 <param name="operation" value="analysis"/>
173 <param name="input_bbo" value="test.tabular"/>
174 <param name="reference" value="hg19"/>
175 <param name="enable_pred" value="yes"/>
176 <param name="pred_mode" value="NEAREST"/>
177 <output name="nearest_neighbour_pred_bed">
178 <assert_contents>
179 <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" />
180 </assert_contents>
181 </output>
182 </test>
183
184 </tests>
157 <help> 185 <help>
158 <![CDATA[ 186 <![CDATA[
159 187
160 .. class:: infomark 188 .. class:: infomark
161 189