Mercurial > repos > bimib > marea
diff marea-1.0.1/marea_cluster.xml @ 15:d0e7f14b773f draft
Upload 1.0.1
| author | bimib |
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| date | Tue, 01 Oct 2019 06:03:12 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/marea-1.0.1/marea_cluster.xml Tue Oct 01 06:03:12 2019 -0400 @@ -0,0 +1,92 @@ +<tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.1"> + <description>of Reaction Activity Scores - 1.0.1</description> + <macros> + <import>marea_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.23.0">pandas</requirement> + <requirement type="package" version="1.1.0">scipy</requirement> + <requirement type="package" version="0.10.1">cobra</requirement> + <requirement type="package" version="0.21.3">scikit-learn</requirement> + <requirement type="package" version="2.2.2">matplotlib</requirement> + <requirement type="package" version="1.17">numpy</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/marea_cluster.py + --input $input + --tool_dir $__tool_directory__ + --out_log $log + #if $data.clust_type == 'kmeans': + --k_min ${data.k_min} + --k_max ${data.k_max} + --elbow ${data.elbow} + --silhouette ${data.silhouette} + #end if + #if $data.clust_type == 'dbscan': + #if $data.dbscan_advanced.advanced == 'true' + --eps ${data.dbscan_advanced.eps} + --min_samples ${data.dbscan_advanced.min_samples} + #end if + #end if + #if $data.clust_type == 'hierarchy': + --k_min ${data.k_min} + --k_max ${data.k_max} + #end if + ]]> + </command> + <inputs> + <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> + + <conditional name="data"> + <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:"> + <option value="kmeans" selected="true">KMeans</option> + <option value="dbscan">DBSCAN</option> + <option value="hierarchy">Agglomerative Hierarchical</option> + </param> + <when value="kmeans"> + <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> + <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> + <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/> + <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/> + </when> + <when value="dbscan"> + <conditional name="dbscan_advanced"> + <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="false"></when> + <when value="true"> + <param name="eps" argument="--eps" type="float" value="0.5" label="Epsilon - The maximum distance between two samples for one to be considered as in the neighborhood of the other" /> + <param name="min_samples" argument="min_samples" type="integer" value="5" label="Min samples - The number of samples in a neighborhood for a point to be considered as a core point (this includes the point itself)"/> + + </when> + </conditional> + </when> + <when value="hierarchy"> + <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> + <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="log" label="${tool.name} - Log" /> + <collection name="results" type="list" label="${tool.name} - Results"> + <discover_datasets pattern="__name_and_ext__" directory="clustering"/> + </collection> + </outputs> + <help> +<![CDATA[ + +What it does +------------- + + +]]> + </help> + <expand macro="citations" /> +</tool> + +