Mercurial > repos > ebi-gxa > scanpy_parameter_iterator

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-parameter-iterator.xml	Wed Apr 03 11:07:24 2019 -0400
@@ -0,0 +1,86 @@
+<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy1">
+    <description>produce an iteration over a defined parameter</description>
+    <macros>
+      <import>scanpy_macros.xml</import>
+    </macros>
+    <requirements>
+      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	 mkdir outputs;
+    #if str( $input_type.parameter_values ) == "list_comma_separated_values":
+        for param in \$(echo '$input_type.input_values' | sed 's/,/ /g'); do
+          echo \$param > outputs/'$parameter_name'_\$param\.txt;
+         done
+    #else if str( $input_type.parameter_values ) == "step_increase_values":
+	     for param in \$(seq '$input_type.start_value' '$input_type.step' '$input_type.end_value'); do
+	       echo \$param > outputs/'$parameter_name'_\$param\.txt;
+	     done
+    #end if
+	    ]]></command>
+
+    <inputs>
+      <param type="select" name="parameter_name" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
+        <option value="perplexity" selected="True">Perplexity</option>
+        <option value="resolution">Resolution</option>
+      </param>
+      <conditional name="input_type">
+        <param type="select" name="parameter_values" label="Choose the format of the input values" help="step increase values or list of all the parameter values">
+          <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option>
+          <option value="step_increase_values">Step increase values to be iterated</option>
+        </param>
+        <when value="list_comma_separated_values">
+          <param type="text" value="0.1, 0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0" name="input_values" label="User input values" help="List of all comma separated values for the parameter"/>
+        </when>
+        <when value="step_increase_values">
+          <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/>
+          <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/>
+          <param type="float" value="10" name="end_value" label="Ending value" help="Final value for the parameter. The final value is not included if increments of step don't match the last value."/>
+        </when>
+      </conditional>
+    </inputs>
+
+    <outputs>
+      <collection name="parameter_iteration" type="list" label="Parameter iterated">
+        <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
+      </collection>
+    </outputs>
+
+    <tests>
+      <test>
+        <param name="parameter_name" value="perplexity"/>
+         <conditional name="input_type">
+          <param name="parameter_values" value="list_comma_separated_values"/>
+          <param name="input_values" value="1, 5, 10"/>
+        </conditional>
+        <output_collection name="parameter_iteration" count="3">
+          <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/>
+          <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/>
+          <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/>
+        </output_collection>
+      </test>
+    </tests>
+
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Given start, step and end, it will iterate parameters for either perplexity or
+resolution.
+
+**Inputs**
+
+* Parameter name: either Resolution or Perplexity.
+* Starting value: float for Resolution, integer for Perplexity.
+* Step: float for Resolution, integer for Perplexity.
+* End value: float for Resolution, integer for Perplexity.
+
+**Outputs**
+
+* Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution).
+
+@VERSION_HISTORY@
+]]></help>
+ <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros.xml	Wed Apr 03 11:07:24 2019 -0400
@@ -0,0 +1,109 @@
+<macros>
+  <token name="@TOOL_VERSION@">1.3.2</token>
+  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
+  <token name="@PLOT_OPTS@">
+#if $do_plotting.plot
+                  -P output.png
+                  --projectio $do_plotting.projection
+                  --components $do_plotting.components
+    #if $do_plotting.color_by
+                  --color-by $do_plotting.color_by
+    #end if
+    #if $do_plotting.groups
+                  --group $do_plotting.groups
+    #end if
+    #if $do_plotting.use_raw
+                  --use-raw
+    #end if
+    #if $do_plotting.palette
+                  --palette $do_plotting.palette
+    #end if
+    #if $do_plotting.edges
+                  --edges
+    #end if
+    #if $do_plotting.arrows
+                  --arrows
+    #end if
+    #if not $do_plotting.sort_order
+                  --no-sort-order
+    #end if
+    #if $do_plotting.frameoff
+                  --frameoff
+    #end if
+#end if
+  </token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@EXPORT_MTX_OPTS@">
+      ${export_mtx}
+  </token>
+  <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+    ]]></token>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1186/s13059-017-1382-0</citation>
+      <citation type="bibtex">
+	@misc{githubscanpy-scripts,
+	author = {Ni Huang, EBI Gene Expression Team},
+	year = {2018},
+	title = {Scanpy-scripts: command line interface for Scanpy},
+	publisher = {GitHub},
+	journal = {GitHub repository},
+	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
+      }</citation>
+      <yield />
+    </citations>
+  </xml>
+  <xml name="input_object_params">
+    <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
+    <param name="input_format" argument="--input-format" type="select" label="Format of input object">
+      <option value="anndata" selected="true">AnnData format hdf5</option>
+      <option value="loom">Loom format hdf5, current support is incomplete</option>
+    </param>
+  </xml>
+  <xml name="output_object_params">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+      <option value="anndata" selected="true">AnnData format hdf5</option>
+      <option value="loom">Loom format hdf5, current support is defective</option>
+    </param>
+  </xml>
+  <xml name="output_plot_params">
+    <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
+    <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
+    <param name="projection" argument="--projection" type="select" label="Plot projection">
+      <option value="2d" selected="true">2D</option>
+      <option value="3d">3D</option>
+    </param>
+    <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
+    <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
+    <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
+    <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
+    <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
+    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
+    <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
+  </xml>
+  <xml name="export_mtx_params">
+    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
+  </xml>
+  <xml name="export_mtx_outputs">
+    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
+      <filter>export_mtx</filter>
+    </data>
+    <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
+      <filter>export_mtx</filter>
+    </data>
+    <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
+      <filter>export_mtx</filter>
+    </data>
+  </xml>
+</macros>