Mercurial > repos > rnateam > blockclust
diff blockclust.xml @ 12:aab6cf87b40a draft
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 |
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--- a/blockclust.xml Tue Feb 03 08:08:49 2015 -0500 +++ b/blockclust.xml Mon Nov 19 08:10:14 2018 -0500 @@ -1,74 +1,43 @@ -<tool id="blockclust" name="BlockClust" version="1.0.0"> +<tool id="blockclust" name="BlockClust" version="1.1.0"> <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description> <requirements> - <requirement type="package" version="1.0">blockclust</requirement> - <requirement type="package" version="1.1">eden</requirement> - <requirement type="package" version="3.0.3">R</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="12.135">mcl</requirement> - <requirement type="package" version="1.0">blockclust_rlibs</requirement> + <requirement type="package" version="1.1.0">blockclust</requirement> </requirements> - <version_command>echo '1.0'</version_command> - <command> -<![CDATA[ + <version_command>blockclust.py -v</version_command> + <command detect_errors="aggressive"><![CDATA[ + export BLOCKCLUST_DATA_PATH=\$(dirname \$(which blockclust.py))/../share/blockclust_data && + #if str($tool_mode.operation) == "pre": - BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed - #elif str($tool_mode.operation) == "clust": + ln -s '$tool_mode.reads_bam' reads.bam && + ln -f -s '${$tool_mode.reads_bam.metadata.bam_index}' reads.bam.bai && + blockclust.py + -m PRE -bam reads.bam + -tbed '$tags_bed' + #elif str($tool_mode.operation) == "analysis": #set $outputdir = $clusters.files_path - #set $accept_bed=list() - #set $reject_bed=list() - ## prepare annotations - #if str($tool_mode.reference) == "hg19": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed") - #elif str($tool_mode.reference) == "mm10": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed") - #elif str($tool_mode.reference) == "dm3": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed") - #elif str($tool_mode.reference) == "rheMac3": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed") - #elif str($tool_mode.reference) == "panTro4": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed") - #elif str($tool_mode.reference) == "xenTro3": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed") - #elif str($tool_mode.reference) == "celWS235": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed") - #elif str($tool_mode.reference) == "tair10": - $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed") - $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed") - #end if - BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config + blockclust.py + -o ./ + -m ANALYSIS + -f "\$BLOCKCLUST_DATA_PATH/blockclust.config" -t $tool_mode.input_bbo - -a #echo ''.join( $accept_bed ) - -r #echo ''.join( $reject_bed ) - -o $outputdir + -a "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.accept.bed" + -r "\$BLOCKCLUST_DATA_PATH/$tool_mode.reference/${tool_mode.reference}.reject.bed" #if $tool_mode.nochr: -nochr #end if #if str($tool_mode.pred.enable_pred) == "yes": - -p - -pm $tool_mode.pred.pred_mode - -md \$BLOCKCLUST_DATA_PATH/models; - #if str($tool_mode.pred.pred_mode) == "nearest_neighbour": - cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed; - #elif str($tool_mode.pred.pred_mode) == "model_based": - cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed; - #end if - #else: - ; + -c + -cm $tool_mode.pred.pred_mode + -md "\$BLOCKCLUST_DATA_PATH/models" #end if - - cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; - cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; - cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out #elif str($tool_mode.operation) == "post": - BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./; + blockclust.py + -m POST + -cbed '$tool_mode.clusters_bed' + -cs '$tool_mode.cmsearch_out' + -tab '$tool_mode.sim_tab_in' + -rfam "\$BLOCKCLUST_DATA_PATH/rfam_map.txt" + -o ./ #end if ]]> </command> @@ -76,13 +45,13 @@ <conditional name="tool_mode"> <param name="operation" type="select" label="Select mode of operation"> <option value="pre">Pre-processing </option> - <option value="clust">Clustering and classification</option> + <option value="analysis">Clustering and classification</option> <option value="post">Post-processing</option> </param> <when value="pre"> <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" /> </when> - <when value="clust"> + <when value="analysis"> <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" /> <param name="reference" type="select" label="Select reference genome"> <option value="hg19">Human (hg19)</option> @@ -102,8 +71,8 @@ </param> <when value="yes"> <param name="pred_mode" type="select" label="Mode of classification"> - <option value="model_based">Model based</option> - <option value="nearest_neighbour">Nearest neighbour</option> + <option value="MODEL">Model based</option> + <option value="NEAREST">Nearest neighbour</option> </param> </when> </conditional> @@ -118,42 +87,101 @@ <outputs> <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> - <filter> tool_mode["operation"]=="pre"</filter> + <filter>tool_mode["operation"]=="pre"</filter> </data> - <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > - <filter> tool_mode["operation"]=="clust"</filter> + <data format="pdf" name="hclust_plot" from_work_dir="hclust_tree.pdf" label="BlockClust: Hierarchical clustering plot on ${on_string}" > + <filter>tool_mode["operation"]=="analysis"</filter> </data> - <data format="bed" name="clusters" label="BlockClust: BED of predicted clusters on ${on_string}"> - <filter> tool_mode["operation"]=="clust"</filter> + <data format="bed" name="clusters" from_work_dir="mcl_clusters/all_clusters.bed" label="BlockClust: BED of predicted clusters on ${on_string}"> + <filter>tool_mode["operation"]=="analysis"</filter> </data> - <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}"> + <data format="bed" name="model_based_pred_bed" from_work_dir="model_based_predictions.txt" label="BlockClust: Model based predictions BED on ${on_string}"> <filter> (( - tool_mode["operation"] == 'clust' and + tool_mode["operation"] == 'analysis' and tool_mode["pred"]["enable_pred"] == "yes" and - tool_mode["pred"]["pred_mode"] == "model_based" + tool_mode["pred"]["pred_mode"] == "MODEL" + )) + </filter> + </data> + <data format="bed" name="nearest_neighbour_pred_bed" from_work_dir="nearest_neighbour_predictions.txt" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> + <filter> + (( + tool_mode["operation"] == 'analysis' and + tool_mode["pred"]["enable_pred"] == "yes" and + tool_mode["pred"]["pred_mode"] == "NEAREST" )) </filter> </data> - <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}"> - <filter> - (( - tool_mode["operation"] == 'clust' and - tool_mode["pred"]["enable_pred"] == "yes" and - tool_mode["pred"]["pred_mode"] == "nearest_neighbour" - )) - </filter> - </data> - <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> - <filter> tool_mode["operation"]=="clust"</filter> + <data format="tabular" name="sim_tab_out" from_work_dir="discretized.gspan.tab" label="BlockClust: Pairwise similarities on ${on_string}"> + <filter>tool_mode["operation"]=="analysis"</filter> </data> <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" > - <filter> tool_mode["operation"]=="post"</filter> + <filter>tool_mode["operation"]=="post"</filter> </data> <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" > - <filter> tool_mode["operation"]=="post"</filter> + <filter>tool_mode["operation"]=="post"</filter> </data> </outputs> + <tests> + <!-- Test: PRE mode --> + + <test expect_num_outputs="1"> + <param name="operation" value="pre"/> + <param name="reads_bam" value="test.bam"/> + <output name="tags_bed"> + <assert_contents> + <has_text_matching expression="chr6\t26555497\t26555527\ttag_10|1|19\t0.052632\t+" /> + <has_text_matching expression="chr11\t122017275\t122017297\ttag_30|1|3\t0.333333\t-" /> + </assert_contents> + </output> + </test> + + <!-- Test: Clustering only --> + <test expect_num_outputs="3"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="no"/> + <output name="clusters"> + <assert_contents> + <has_text_matching expression="chr1\t173833959\t173834043\t10:snoRNA_CD-box:blockgroup_939:cluster_1\t451.50\t-" /> + <has_text_matching expression="chr13\t92003008\t92003075\t8:miRNA:blockgroup_256:cluster_3\t2950.50\t\+" /> + </assert_contents> + </output> + </test> + + <!-- Test: Model based prediction --> + + <test expect_num_outputs="4"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="yes"/> + <param name="pred_mode" value="MODEL"/> + <output name="model_based_pred_bed"> + <assert_contents> + <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" /> + </assert_contents> + </output> + </test> + + <!-- Test: Nearest neighbour based prediction --> + + <test expect_num_outputs="4"> + <param name="operation" value="analysis"/> + <param name="input_bbo" value="test.tabular"/> + <param name="reference" value="hg19"/> + <param name="enable_pred" value="yes"/> + <param name="pred_mode" value="NEAREST"/> + <output name="nearest_neighbour_pred_bed"> + <assert_contents> + <has_text_matching expression="chr2\t203211000\t203211097\tpredicted_tRNA\t284.07\t-" /> + </assert_contents> + </output> + </test> + + </tests> <help> <![CDATA[