changeset 0:b7bd78670961 draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 3fc448754d6720855f781caa7938e33d3961b092"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sccaf_macros.xml	Thu Apr 16 09:18:27 2020 +0000
@@ -0,0 +1,102 @@
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement>
+    </requirements>
+  </xml>
+  <token name="@TOOL_VERSION@">0.0.9</token>
+  <token name="@SCCAF_INTRO@">
+SCCAF explained
+===============
+
+Single Cell Clustering Assessment Framework (SCCAF) is a novel method for
+automated identification of putative cell types from single cell RNA-seq
+(scRNA-seq) data. By iteratively applying clustering and a machine learning
+approach to gene expression profiles of a given set of cells, SCCAF
+simultaneously identifies distinct cell groups and a weighted list of feature
+genes for each group. The feature genes, which are overexpressed in the
+particular cell group, jointly discriminate the given cell group from other
+cells. Each such group of cells corresponds to a putative cell type or state,
+characterised by the feature genes as markers.
+  </token>
+  <token name="@HELP@">More information can be found at https://github.com/SCCAF/SCCAF</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.show_edges
+                  --edges
+    #end if
+    #if $do_plotting.show_arrows
+                  --arrows
+    #end if
+    #if not $do_plotting.color_order
+                  --no-sort-order
+    #end if
+    #if $do_plotting.omit_frame
+                  --frameoff
+    #end if
+#end if
+  </token>
+  <xml name="citations">
+    <citations>
+      <citation type="doi"></citation>
+      <citation type="bibtex">
+	@misc{githubsccaf,
+	author = {Miao, Zhichao},
+	year = {2018},
+	title = {SCCAF},
+	publisher = {GitHub},
+	journal = {GitHub repository},
+	url = {https://github.com/Functional-Genomics/SCCAF},
+      }</citation>
+      <citation type="doi">10.1101/2020.04.08.032698</citation>
+      <yield />
+    </citations>
+  </xml>
+  <xml name="input_object_params">
+    <param name="input_obj_file" argument="--input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/>
+  </xml>
+  <xml name="output_object_params">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+      <option value="anndata_h5ad" selected="true">AnnData format hdf5</option>
+      <option value="anndata">AnnData format (h5 for older versions)</option>
+    </param>
+  </xml>
+  <xml name="output_data_obj" token_description="operation">
+    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata_h5ad'</filter>
+    </data>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata'</filter>
+    </data>
+  </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="show_edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
+    <param name="show_arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
+    <param name="color_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
+    <param name="omit_frame" argument="--frameoff" type="boolean" checked="false" label="Show frame"/>
+  </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sccaf_regress_out.xml	Thu Apr 16 09:18:27 2020 +0000
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy1">
+  <description>with multiple categorical keys on an AnnData object.</description>
+  <macros>
+    <import>sccaf_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+  ln -s '${input_obj_file}' input.h5 &&
+  sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}'
+  ]]></command>
+  <inputs>
+    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/>
+    <expand macro="output_object_params"/>
+    <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/>
+  </inputs>
+  <outputs>
+    <expand macro="output_data_obj" description="regressed out on ${keys_to_regress}"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="color_by" value="louvain"/>
+      <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=============================
+Operations on AnnData objects
+=============================
+
+Performs the following operations:
+
+* Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one.
+* Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of genes.
+* For the flags created, calculates qc metrics (pct_<flag>_counts).
+* Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
+* For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes).
+
+This functionality will probably be added in the future to a larger package.
+]]></help>
+  <!-- <expand macro="citations"/> -->
+</tool>

Binary file static/images/example_sccaf_workflow.png has changed