| Previous changeset 3:d10410cfd17a (2017-02-27) Next changeset 5:9b5fb987a484 (2017-03-17) |
|
Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923 |
|
modified:
NSPDK_candidateClusters.xml NSPDK_sparseVect.xml |
| b |
| diff -r d10410cfd17a -r 0625db6b6e45 NSPDK_candidateClusters.xml --- a/NSPDK_candidateClusters.xml Mon Feb 27 12:03:12 2017 -0500 +++ b/NSPDK_candidateClusters.xml Mon Mar 13 18:05:04 2017 -0400 |
| [ |
| b'@@ -1,113 +1,123 @@\n <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">\n-\t<requirements>\n-\t\t<requirement type="package" version="0.1.8">graphclust-wrappers</requirement>\n-\t\t<requirement type="package" version="0.5">perl-array-utils</requirement>\n-\t\t<requirement type="package" version="9.2">nspdk</requirement>\n-\t</requirements>\n-\t<stdio>\n-\t\t<exit_code range="1:" />\n-\t</stdio>\n-\t<command>\n-\t\t<![CDATA[\n+ <requirements>\n+ <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>\n+ <requirement type="package" version="0.5">perl-array-utils</requirement>\n+ <requirement type="package" version="9.2">nspdk</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[\n \n- mkdir -p SVECTOR &&\n-\n- cp $data_svector SVECTOR/data.svector &&\n-\n- \'NSPDK_candidateClusters.pl\' \'$data_fasta\' \'$data_names\' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations\n+ mkdir ./SVECTOR &&\n \n- #if $iteration_num.iteration_num_selector:\n- $iteration_num.CI\n- \'$blacklist\'\n- \'$final_partition_soft\'\n- \'$fast_cluster_last_round\'\n- $iteration_num.GLOBAL_hit_blacklist_overlap\n+ #for $ins in $data_svector:\n+ ln -f -s \'$ins\' ./SVECTOR/ &&\n+ #end for\n \n- #else:\n- 1\n-\n- #end if\n+ NSPDK_candidateClusters.pl\n+ \'$data_fasta\'\n+ \'$data_names\'\n+ $noCache\n+ $ensf\n+ $oc\n+ $usn\n+ $knn\n+ $nhf\n+ $nspdk_nhf_max\n+ $nspdk_nhf_step\n+ $GLOBAL_num_clusters\n+ $max_rad\n+ $max_dist_relations\n \n-]]>\n-\t</command>\n-\t<inputs>\n-\t\t<param type="data" name="data_svector" format="zip" />\n-\t\t<param type="data" name="data_fasta" format="fasta" />\n-\t\t<param type="data" name="data_names" format="txt" />\n-\t\t<conditional name="iteration_num">\n-\t\t\t<param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>\n-\t\t\t<when value="true">\n-\t\t\t\t<param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>\n-\t\t\t\t<param type="data" name="blacklist" format="txt" />\n-\t\t\t\t<param type="data" name="final_partition_soft" format="txt" />\n-\t\t\t\t<param type="data" name="fast_cluster_last_round" format="txt" />\n-\t\t\t\t<param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />\n-\t\t\t</when>\n-\t\t\t<when value="false" >\n-\t\t\t\t<param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>\n-\t\t\t</when>\n-\t\t</conditional>\n-\t\t<param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>\n-\t\t<param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>\n-\t\t<param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"\n+ #if $iteration_num.iteration_num_selector:\n+ $iteration_num.CI\n+ \'$blacklist\'\n+ \'$final_partition_soft\'\n+ \'$fast_cluster_last_round\'\n+ $iteration_num.GLOBAL_hit_blacklist_overlap\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param type="data" name="data_svector" multiple="True"/>\n+ <param type="data" name="data_fasta" format="fasta" />\n+ <param type="data" name="data_names" format="txt" />\n+ <conditional name="iteration_num">\n+ <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>\n+ <when value="true">\n+ <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>\n+ <param type="data" name="blac'..b'arest neighbors" help="-knn num"/>\n+ <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>\n+ <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />\n+ <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/>\n+ <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />\n+ </inputs>\n+ <outputs>\n+ <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is False</filter>\n+ </data>\n+ <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is False </filter>\n+ </data>\n+ <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is False </filter>\n+ </data>\n+ <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is True</filter>\n+ </data>\n+ <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is True</filter>\n+ </data>\n+ <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >\n+ <filter> iteration_num[\'iteration_num_selector\'] is True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="data_fasta" value="data.fasta"/>\n+ <param name="data_names" value="data.names"/>\n+ <param name="data_svector" value="data.svector.1" ftype="zip" />\n+ <conditional name="iteration_num">\n+ <param name="iteration_num_selector" value="false"/>\n+ </conditional>\n+ <param name="noCache" value="-no-cache"/>\n+ <param name="ensf" value="5"/>\n+ <param name="oc" value="-oc"/>\n+ <param name="max_rad" value="3"/>\n+ <param name="max_dist_relations" value="3"/>\n+ <param name="usn" value="-usn"/>\n+ <param name="knn" value="20"/>\n+ <param name="nhf" value="500"/>\n+ <param name="nspdk_nhf_max" value="1000"/>\n+ <param name="nspdk_nhf_step" value="25"/>\n+ <param name="GLOBAL_num_clusters" value="100"/>\n+ <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />\n+ <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />\n+ <output name="black_list" file="SVECTOR/data.svector.blacklist.1" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n \n **What it does**\n \n@@ -133,10 +143,10 @@\n \n \n ]]>\n-\t</help>\n-\t<citations>\n-\t\t<citation type="doi">10.1093/bioinformatics/bts224</citation>\n-\t\t<citation type="bibtex">@inproceedings{costa2010fast,\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/bts224</citation>\n+ <citation type="bibtex">@inproceedings{costa2010fast,\n title={Fast neighborhood subgraph pairwise distance kernel},\n author={Costa, Fabrizio and De Grave, Kurt},\n booktitle={Proceedings of the 26th International Conference on Machine Learning},\n@@ -145,5 +155,5 @@\n organization={Omnipress}\n }\n </citation>\n-\t</citations>\n+ </citations>\n </tool>\n' |
| b |
| diff -r d10410cfd17a -r 0625db6b6e45 NSPDK_sparseVect.xml --- a/NSPDK_sparseVect.xml Mon Feb 27 12:03:12 2017 -0500 +++ b/NSPDK_sparseVect.xml Mon Mar 13 18:05:04 2017 -0400 |
| [ |
| @@ -1,39 +1,43 @@ <tool id="nspdk_sparse" name="NSPDK_sparseVect" version="9.2"> - <requirements> - <requirement type="package" version="0.1.9">graphclust-wrappers</requirement> - <requirement type="package" version="9.2">nspdk</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ + <requirements> + <requirement type="package" version="0.1.10">graphclust-wrappers</requirement> + <requirement type="package" version="9.2">nspdk</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ - 'NSPDK_sparseVect.pl' '$data_fasta' '$gspan_file' $max_rad $max_dist_relations + NSPDK_sparseVect.pl + '$data_fasta' + '$gspan_file' + $max_rad + $max_dist_relations ]]> - </command> - <inputs> - <param type="data" name="gspan_file" format="searchgui_archive" /> - <param type="data" name="data_fasta" format="fasta" /> - <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> - <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> - </inputs> - <outputs> - <data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/> - </outputs> - <tests> - <test> - <param name="data_fasta" value="data.fasta"/> - <param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/> - <param name="max_rad" value="3"/> - <param name="max_dist_relations" value="3"/> - <output name="data_svector" file="SVECTOR/data.svector" ftype="zip" /> - </test> - </tests> - <help> - <![CDATA[ + </command> + <inputs> + <param type="data" name="gspan_file" /> + <param type="data" name="data_fasta" format="fasta" /> + <param name="max_rad" type="integer" value="3" label="maximum radius " help="-R"/> + <param name="max_dist_relations" type="integer" value="3" label="maximum distance relations" help="-D"/> + </inputs> + <outputs> + <data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/> + </outputs> + <tests> + <test> + <param name="data_fasta" value="data.fasta"/> + <param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/> + <param name="max_rad" value="3"/> + <param name="max_dist_relations" value="3"/> + <output name="data_svector" file="SVECTOR/data.svector" ftype="zip" /> + </test> + </tests> + <help> + <![CDATA[ **What it does** @@ -45,22 +49,22 @@ **Parameters** -+ **-R** <max radius> (default: 1) -+ **-D** <max distance relations> (default: 4) ++ **-R** <max radius> (default: 1) ++ **-D** <max distance relations> (default: 4) ]]> - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/bts224</citation> - <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> - </citations> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts224</citation> + <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> + </citations> </tool> |