diff sccaf_regress_out.xml @ 0:885db50f1bc1 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sccaf_regress_out.xml	Tue Nov 19 13:06:04 2019 -0500
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy0">
+  <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"/>
+    <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>
+    <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: regressesed 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" 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>