Mercurial > repos > ebi-gxa > scmap_scmap_cluster

changeset 0:5421e01f640a draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author ebi-gxa
date Mon, 16 Sep 2019 09:58:40 -0400
parents
children b436e7d353ae
files scmap_macros.xml scmap_scmap_cluster.xml test-data/closest_cells.csv test-data/closest_cells_clusters.csv test-data/closest_cells_clusters.rds test-data/closest_cells_similarities.csv test-data/index_cell.rds test-data/index_cluster.png test-data/index_cluster.rds test-data/project_cluster.csv test-data/project_cluster.rds test-data/select_features.png test-data/select_features.rds test-data/test_sce.rds
diffstat 14 files changed, 185 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_macros.xml	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,43 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.6.0</token>
+    <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.2">scmap-cli</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", scmap version" $(R --vanilla --slave -e "library(scmap); cat(sessionInfo()\$otherPkgs\$scmap\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @Article{,
+            title = {scmap - A tool for unsupervised projection of single cell RNA-seq data},
+            author = {Vladimir Yu. Kiselev and Martin Hemberg},
+            year = {2017},
+            journal = {bioRxiv},
+            url = {http://doi.org/10.1101/150292},
+          }
+        </citation>
+        <citation type="bibtex">
+          @misc{githubscmap-cli.git,
+            author = {Jonathan Manning, EBI Gene Expression Team},
+            year = {2018},
+            title = {scmap-cli: command line interface for scmap},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/scmap-cli.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_scmap_cluster.xml	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,33 @@
+<tool id="scmap_scmap_cluster" name="scmap cluster projection" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <description>projects one dataset to another</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-scmap-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
+    ]]></command>
+    <inputs>
+        <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
+        <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
+        <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
+    </inputs>
+    <outputs>
+        <data name="output_single_cell_experiment" format="rdata" />
+        <data name="output_txt" format="csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
+            <output name="output_single_cell_experiment" file="project_cluster.rds"/>
+            <output name="output_txt" file="project_cluster.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells.csv	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,6 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_clusters.csv	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,6 @@
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Binary file test-data/closest_cells_clusters.rds has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_similarities.csv	Mon Sep 16 09:58:40 2019 -0400
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Binary file test-data/index_cell.rds has changed
Binary file test-data/index_cluster.png has changed
Binary file test-data/index_cluster.rds has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.csv	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,91 @@
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