changeset 0:2142ecf6ff02 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/garnett_macros.xml	Wed Apr 08 06:18:13 2020 -0400
@@ -0,0 +1,44 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.2.8</token>
+    <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.0.3">garnett-cli</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command><![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", garnett version" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+    **Version history**
+    0.2.8+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{,
+                url = {https://doi.org/10.1038/s41592-019-0535-3},           
+                author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
+                title = {Supervised classification enables rapid annotation of cell atlases},
+                journal = {Nature Methods}
+            }
+        </citation>
+            <citation type="bibtex">
+                @misc{githubgarnett-cli.git,
+                    author = {Andrey Solovyev, EBI Gene Expression Team},
+                    year = {2019},
+                    title = {garnett-cli: command line interface for Garnett tool},
+                    publisher = {GitHub},
+                    journal = {GitHub repository},
+                    url = {https://github.com/ebi-gene-expression-group/garnett-cli.git},
+                  }
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/garnett_transform_markers.xml	Wed Apr 08 06:18:13 2020 -0400
@@ -0,0 +1,35 @@
+<tool id="garnett_transform_markers" name="Garnett - transform markes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett</description>
+    <macros>
+        <import>garnett_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}' --pval-col '${pval_col}' --pval-threshold '${pval_threshold}' --groups-col '${groups_col}' --gene-names '${gene_names}' --garnett-marker-file '${garnett_marker_file}'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" />
+        <param type="data" name="marker_list" format="rdata" label="Marker list object" help="Path to a serialised object containing marker genes" />
+        <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" />
+        <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" />
+        <param type="text" name="groups_col" value="groups" label="groups column" help="Column name of cell groups (i.e. cluster IDs or cell types) in marker file" />
+        <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" />
+    </inputs>
+    <outputs>
+        <data name="garnett_marker_file" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_marker_file" value="ref_marker_genes.txt" />
+            <param name="marker_list" value="marker_list.rds" />
+            <output name="garnett_marker_file" file="markers_transformed.txt" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+         @HELP@
+
+        @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+