diff scanpy-run-dpt.xml @ 0:f57f57c459d8 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-run-dpt.xml	Mon Sep 16 08:24:32 2019 -0400
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0">
+  <description>diffusion pseudotime inference</description>
+  <macros>
+    <import>scanpy_macros2.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-cli dpt
+    --n-dcs $n_dcs
+    --root '${root_attr}' '${root_value}'
+#if $n_branchings > 0
+    --n-branchings ${n_branchings}
+    --min-group-size ${min_group_size}
+#end if
+#if $use_graph
+    --use-graph '${use_graph}'
+#end if
+#if $key_added
+    --key-added '${key_added}'
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+
+    <param name="n_dcs" argument="--n-dcs" type="integer" min="2" value="10"
+           label="Number of diffusion components to use"/>
+    <param name="n_branchings" argument="--n-branchings" min="0" type="integer" value="0"
+           label="Number of branchings to detect"/>
+    <param name="min_group_size" argument="--min-group-size" type="float" min="0" max="1" value="0"
+           label="The fraction of total cells under which further splitting is skipped during recursive splitting of branches"
+           help="Ignored when `Number of branchings to detect` is 0"/>
+    <param name="root_attr" argument="--root {attr} value" type="text"
+           label="Name of attribute that defines clustering"/>
+    <param name="root_value" argument="--root attr {value}" type="text"
+           label="Name of the clustering that defines the root cell type"/>
+    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+           label="Name of the slot that holds the KNN graph"/>
+    <param name="key_added" argument="--key-added" type="text" optional="true"
+           label="Additional suffix to the name of the slot to save the calculated trajectory"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: dpt object"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="diffmap.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="n_dcs" value="10"/>
+      <param name="root_attr" value="leiden"/>
+      <param name="root_value" value="1"/>
+      <param name="use_graph" value="neighbors"/>
+      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+================================================
+Calculate Diffusion Pseudotime (`scanpy.tl.dpt`)
+================================================
+
+Calculate diffusion pseudotime from single cell KNN graphs.
+
+This requires to run `Scanpy DiffusionMap` and `Scanpy FindCluster`, first.
+
+It yields `dpt_pseudotime`, diffusion pseudotime as an attribute for each cell.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations">
+    <citation type="doi">10.1186/s13059-019-1663-x</citation>
+  </expand>
+</tool>