Mercurial > repos > rnateam > graphclust_postprocessing
diff glob_report.xml @ 17:f93c868203cc draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
| author | rnateam |
|---|---|
| date | Sat, 27 Oct 2018 13:23:06 -0400 |
| parents | 79df97a1bc0f |
| children |
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--- a/glob_report.xml Fri Feb 23 10:46:41 2018 -0500 +++ b/glob_report.xml Sat Oct 27 13:23:06 2018 -0400 @@ -1,46 +1,32 @@ -<tool id="glob_report" name="cluster_collection_report" version="0.4" > +<tool id="glob_report" name="cluster_collection_report" version="0.5" > <requirements> - <requirement type="package" version="0.5.2">graphclust-wrappers</requirement> + <requirement type="package" version="0.6.0">graphclust-wrappers</requirement> <requirement type="package" version='0.5'>perl-array-utils</requirement> <requirement type="package" version='0.18.1'>scikit-learn</requirement> <requirement type="package" version='1.8.10'>locarna</requirement> <requirement type="package" version='2.1'>rnaz</requirement> <requirement type="package" version="1.1.2">infernal</requirement> <requirement type="package" version='2.2.10'>viennarna</requirement> - <requirement type="package" version='1.3.26'>graphicsmagick</requirement> + <requirement type="package" version='1.3.30'>graphicsmagick</requirement> <requirement type="package" version='0.6.1'>rscape</requirement> <requirement type="package" version='6.0'>unzip</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ + <command detect_errors="exit_code"> + <![CDATA[ unzip $FASTA &> /dev/null && - - mkdir ./CMSEARCH && - mkdir ./MODEL && - - #set $inputFiles = "" - + mkdir ./CMSEARCH && + mkdir ./MODEL && + #import re #for $cms_res in $cmsearch_results: - ###set $inputFiles += str($cms_res.element_identifier)+',' - ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier && + #set $safename_cm = re.sub('[^\w\-_\.]', '_', $cms_res.element_identifier) + ln -f -s '$cms_res' ./CMSEARCH/$safename_cm && #end for - #set $inputFiles = $inputFiles[:-1] - - #set $inputFilesTrees = "" - #for $mods in $model_tree_files: - ###set $inputFilesTrees += str($mods.element_identifier)+',' - ln -f -s '$mods' ./MODEL/$mods.element_identifier && + #set $safename_tr = re.sub('[^\w\-_\.]', '_', $mods.element_identifier) + ln -f -s '$mods' ./MODEL/$safename_tr && #end for - #set $inputFilesTrees = $inputFilesTrees[:-1] - 'glob_res.pl' - ##'$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size @@ -49,7 +35,6 @@ $cm_bitscore_sig $partition_type '' $cut_type - ##'$inputFilesTrees' $results_top_num #if $iteration_num.iteration_num_selector: $iteration_num.CI @@ -157,7 +142,10 @@ <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> <collection name="clusters" type="list" label="CLUSTERS"> - <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> + <discover_datasets format="txt" pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> + </collection> + <collection name="allFasta" type="list" label="sequences.fa"> + <discover_datasets format="fasta" pattern="(?P<name>^.*\.all.fa$)" directory="RESULTS" /> </collection> <collection name="partitions" type="list" label="Partitions"> <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> @@ -178,7 +166,6 @@ <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> <param name="cmsearch_results" value="1.1.tree,1.2.tree"/> <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> - <param name="combined_cm_out" value="combined_cm_out"/> <param name="partition_type" value="0"/> <param name="cut_type" value="0"/> <conditional name="iteration_num"> @@ -190,11 +177,13 @@ <param name="cm_min_bitscore" value="20"/> <param name="cm_max_eval" value="0.001"/> <param name="cm_bitscore_sig" value="0"/> + <param name="results_top_num" value="5"/> <output name="final_stats" file="RESULTS/cluster.final.stats" /> + <output name="combined_cm_out" file="combined_cm_out"/> + <output name="evaluation" file="evaluation1.txt"/> <output_collection name="clusters" type="list"> <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> - <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> - + <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> </output_collection> <output_collection name="partitions"> <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> @@ -215,7 +204,6 @@ <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> </output_collection> - <param name="results_top_num" value="5"/> <output_collection name="topSecondaryStruct" type="list"> <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> @@ -247,14 +235,6 @@ ]]> </help> <citations> - <citation type="bibtex">@inproceedings{costa2010fast, - title={Fast neighborhood subgraph pairwise distance kernel}, - author={Costa, Fabrizio and De Grave, Kurt}, - booktitle={Proceedings of the 26th International Conference on Machine Learning}, - pages={255--262}, - year={2010}, - organization={Omnipress} - } - </citation> + <citation type="doi">10.5281/zenodo.597695</citation> </citations> </tool>