# HG changeset patch
# User ebi-gxa
# Date 1568642320 14400
# Node ID 5421e01f640aeb07fd47776be79ae210b9110281

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"

diff -r 000000000000 -r 5421e01f640a scmap_macros.xml
--- /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" $(R --vanilla --slave -e "library(scmap); cat(sessionInfo()\$otherPkgs\$scmap\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @Article{,
+            title = {scmap - A tool for unsupervised projection of single cell RNA-seq data},
+            author = {Vladimir Yu. Kiselev and Martin Hemberg},
+            year = {2017},
+            journal = {bioRxiv},
+            url = {http://doi.org/10.1101/150292},
+          }
+        </citation>
+        <citation type="bibtex">
+          @misc{githubscmap-cli.git,
+            author = {Jonathan Manning, EBI Gene Expression Team},
+            year = {2018},
+            title = {scmap-cli: command line interface for scmap},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/scmap-cli.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 5421e01f640a scmap_scmap_cluster.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_scmap_cluster.xml	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,33 @@
+<tool id="scmap_scmap_cluster" name="scmap cluster projection" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <description>projects one dataset to another</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-scmap-cluster.R --index-object-file '$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>
diff -r 000000000000 -r 5421e01f640a test-data/closest_cells.csv
--- /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 @@
+,Oocyte..1.RPKM.,Oocyte..2.RPKM.,Oocyte..3.RPKM.,Zygote..1.RPKM.,Zygote..2.RPKM.,Zygote..3.RPKM.,X2.cell.embryo.1..Cell.1.RPKM.,X2.cell.embryo.1..Cell.2.RPKM.,X2.cell.embryo.2..Cell.1.RPKM.,X2.cell.embryo.2..Cell.2.RPKM.,X2.cell.embryo.3..Cell.1.RPKM.,X2.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.1..Cell.1.RPKM.,X4.cell.embryo.1..Cell.2.RPKM.,X4.cell.embryo.1..Cell.3.RPKM.,X4.cell.embryo.1..Cell.4.RPKM.,X4.cell.embryo.2..Cell.1.RPKM.,X4.cell.embryo.2..Cell.2.RPKM.,X4.cell.embryo.2..Cell.3.RPKM.,X4.cell.embryo.2..Cell.4.RPKM.,X4.cell.embryo.3..Cell.1.RPKM.,X4.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.3..Cell.3.RPKM.,X4.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.1..Cell.1.RPKM.,X8.cell.embryo.1..Cell.2.RPKM.,X8.cell.embryo.1..Cell.3.RPKM.,X8.cell.embryo.1..Cell.4.RPKM.,X8.cell.embryo.2..Cell.1.RPKM.,X8.cell.embryo.2..Cell.2.RPKM.,X8.cell.embryo.2..Cell.3.RPKM.,X8.cell.embryo.2..Cell.4.RPKM.,X8.cell.embryo.2..Cell.5.RPKM.,X8.cell.embryo.2..Cell.6.RPKM.,X8.cell.embryo.2..Cell.7.RPKM.,X8.cell.embryo.2..Cell.8.RPKM.,X8.cell.embryo.3..Cell.1.RPKM.,X8.cell.embryo.3..Cell.2.RPKM.,X8.cell.embryo.3..Cell.3.RPKM.,X8.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.3..Cell.5.RPKM.,X8.cell.embryo.3..Cell.6.RPKM.,X8.cell.embryo.3..Cell.7.RPKM.,X8.cell.embryo.3..Cell.8.RPKM.,Morulae..1..Cell.1.RPKM.,Morulae..1..Cell.2.RPKM.,Morulae..1..Cell.3.RPKM.,Morulae..1..Cell.4.RPKM.,Morulae..1..Cell.5.RPKM.,Morulae..1..Cell.6.RPKM.,Morulae..1..Cell.7.RPKM.,Morulae..1..Cell.8.RPKM.,Morulae..2..Cell.1.RPKM.,Morulae..2..Cell.2.RPKM.,Morulae..2..Cell.3.RPKM.,Morulae..2..Cell.4.RPKM.,Morulae..2..Cell.5.RPKM.,Morulae..2..Cell.6.RPKM.,Morulae..2..Cell.7.RPKM.,Morulae..2..Cell.8.RPKM.,Late.blastocyst..1..Cell.1.RPKM.,Late.blastocyst..1..Cell.2.RPKM.,Late.blastocyst..1..Cell.3.RPKM.,Late.blastocyst..1..Cell.4.RPKM.,Late.blastocyst..1..Cell.5.RPKM.,Late.blastocyst..1..Cell.6.RPKM.,Late.blastocyst..1..Cell.7.RPKM.,Late.blastocyst..1..Cell.8.RPKM.,Late.blastocyst..1..Cell.9.RPKM.,Late.blastocyst..1..Cell.10.RPKM.,Late.blastocyst..1..Cell.11.RPKM.,Late.blastocyst..1..Cell.12.RPKM.,Late.blastocyst..2..Cell.1.RPKM.,Late.blastocyst..2..Cell.2.RPKM.,Late.blastocyst..2..Cell.3.RPKM.,Late.blastocyst..2..Cell.4.RPKM.,Late.blastocyst..2..Cell.5.RPKM.,Late.blastocyst..2..Cell.6.RPKM.,Late.blastocyst..2..Cell.7.RPKM.,Late.blastocyst..2..Cell.8.RPKM.,Late.blastocyst..2..Cell.9.RPKM.,Late.blastocyst..2..Cell.10.RPKM.,Late.blastocyst..3..Cell.1.RPKM.,Late.blastocyst..3..Cell.2.RPKM.,Late.blastocyst..3..Cell.3.RPKM.,Late.blastocyst..3..Cell.4.RPKM.,Late.blastocyst..3..Cell.5.RPKM.,Late.blastocyst..3..Cell.6.RPKM.,Late.blastocyst..3..Cell.7.RPKM.,Late.blastocyst..3..Cell.8.RPKM.
+1,1,1,1,6,6,6,10,10,10,10,12,10,23,19,24,22,14,13,24,13,21,24,23,24,28,27,27,25,34,35,36,32,34,34,35,30,37,42,44,38,38,37,39,39,48,49,47,49,46,49,49,27,57,54,55,55,54,51,55,54,62,67,67,63,71,67,62,66,69,69,71,78,65,87,84,78,78,81,82,82,78,81,88,84,90,75,83,78,88,88
+2,2,2,2,11,12,11,7,7,7,7,7,7,13,13,13,14,24,22,14,20,22,23,21,21,27,25,25,27,36,30,30,34,30,33,34,36,38,37,39,39,42,38,43,43,45,46,52,45,51,54,51,26,49,57,56,59,57,59,56,60,70,71,62,67,62,71,69,62,72,62,63,70,76,86,86,81,79,78,76,80,82,82,87,88,89,74,74,88,85,90
+3,3,3,3,12,10,12,8,8,8,8,8,11,14,24,23,21,19,16,19,23,23,18,22,22,26,26,26,26,30,36,34,36,33,36,36,35,40,40,40,41,40,40,38,44,49,54,26,51,54,51,50,28,51,50,59,60,53,58,58,53,61,61,63,64,69,66,64,82,70,70,72,81,71,75,75,76,81,76,78,76,81,78,75,80,88,86,86,90,77,81
+4,6,7,6,4,11,4,9,9,9,9,9,12,24,14,16,16,23,18,23,18,24,13,13,13,40,38,40,38,29,29,29,29,29,29,29,29,42,38,38,37,37,42,37,41,51,50,28,48,50,50,53,47,54,53,54,58,60,56,54,50,71,68,82,65,65,68,67,68,67,65,65,72,73,73,80,82,82,79,79,75,76,79,86,73,85,83,87,89,89,85
+5,5,5,5,5,5,5,12,12,12,12,11,5,22,23,15,24,17,21,17,22,18,22,24,23,25,28,28,28,31,31,31,35,36,35,31,31,41,41,41,40,41,41,41,38,53,51,27,50,49,46,46,52,53,51,58,56,51,55,59,51,65,62,71,72,70,72,66,78,65,72,69,65,70,74,74,79,77,82,77,84,72,76,83,75,72,87,75,85,90,89
diff -r 000000000000 -r 5421e01f640a test-data/closest_cells_clusters.csv
--- /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 @@
+,Oocyte..1.RPKM.,Oocyte..2.RPKM.,Oocyte..3.RPKM.,Zygote..1.RPKM.,Zygote..2.RPKM.,Zygote..3.RPKM.,X2.cell.embryo.1..Cell.1.RPKM.,X2.cell.embryo.1..Cell.2.RPKM.,X2.cell.embryo.2..Cell.1.RPKM.,X2.cell.embryo.2..Cell.2.RPKM.,X2.cell.embryo.3..Cell.1.RPKM.,X2.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.1..Cell.1.RPKM.,X4.cell.embryo.1..Cell.2.RPKM.,X4.cell.embryo.1..Cell.3.RPKM.,X4.cell.embryo.1..Cell.4.RPKM.,X4.cell.embryo.2..Cell.1.RPKM.,X4.cell.embryo.2..Cell.2.RPKM.,X4.cell.embryo.2..Cell.3.RPKM.,X4.cell.embryo.2..Cell.4.RPKM.,X4.cell.embryo.3..Cell.1.RPKM.,X4.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.3..Cell.3.RPKM.,X4.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.1..Cell.1.RPKM.,X8.cell.embryo.1..Cell.2.RPKM.,X8.cell.embryo.1..Cell.3.RPKM.,X8.cell.embryo.1..Cell.4.RPKM.,X8.cell.embryo.2..Cell.1.RPKM.,X8.cell.embryo.2..Cell.2.RPKM.,X8.cell.embryo.2..Cell.3.RPKM.,X8.cell.embryo.2..Cell.4.RPKM.,X8.cell.embryo.2..Cell.5.RPKM.,X8.cell.embryo.2..Cell.6.RPKM.,X8.cell.embryo.2..Cell.7.RPKM.,X8.cell.embryo.2..Cell.8.RPKM.,X8.cell.embryo.3..Cell.1.RPKM.,X8.cell.embryo.3..Cell.2.RPKM.,X8.cell.embryo.3..Cell.3.RPKM.,X8.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.3..Cell.5.RPKM.,X8.cell.embryo.3..Cell.6.RPKM.,X8.cell.embryo.3..Cell.7.RPKM.,X8.cell.embryo.3..Cell.8.RPKM.,Morulae..1..Cell.1.RPKM.,Morulae..1..Cell.2.RPKM.,Morulae..1..Cell.3.RPKM.,Morulae..1..Cell.4.RPKM.,Morulae..1..Cell.5.RPKM.,Morulae..1..Cell.6.RPKM.,Morulae..1..Cell.7.RPKM.,Morulae..1..Cell.8.RPKM.,Morulae..2..Cell.1.RPKM.,Morulae..2..Cell.2.RPKM.,Morulae..2..Cell.3.RPKM.,Morulae..2..Cell.4.RPKM.,Morulae..2..Cell.5.RPKM.,Morulae..2..Cell.6.RPKM.,Morulae..2..Cell.7.RPKM.,Morulae..2..Cell.8.RPKM.,Late.blastocyst..1..Cell.1.RPKM.,Late.blastocyst..1..Cell.2.RPKM.,Late.blastocyst..1..Cell.3.RPKM.,Late.blastocyst..1..Cell.4.RPKM.,Late.blastocyst..1..Cell.5.RPKM.,Late.blastocyst..1..Cell.6.RPKM.,Late.blastocyst..1..Cell.7.RPKM.,Late.blastocyst..1..Cell.8.RPKM.,Late.blastocyst..1..Cell.9.RPKM.,Late.blastocyst..1..Cell.10.RPKM.,Late.blastocyst..1..Cell.11.RPKM.,Late.blastocyst..1..Cell.12.RPKM.,Late.blastocyst..2..Cell.1.RPKM.,Late.blastocyst..2..Cell.2.RPKM.,Late.blastocyst..2..Cell.3.RPKM.,Late.blastocyst..2..Cell.4.RPKM.,Late.blastocyst..2..Cell.5.RPKM.,Late.blastocyst..2..Cell.6.RPKM.,Late.blastocyst..2..Cell.7.RPKM.,Late.blastocyst..2..Cell.8.RPKM.,Late.blastocyst..2..Cell.9.RPKM.,Late.blastocyst..2..Cell.10.RPKM.,Late.blastocyst..3..Cell.1.RPKM.,Late.blastocyst..3..Cell.2.RPKM.,Late.blastocyst..3..Cell.3.RPKM.,Late.blastocyst..3..Cell.4.RPKM.,Late.blastocyst..3..Cell.5.RPKM.,Late.blastocyst..3..Cell.6.RPKM.,Late.blastocyst..3..Cell.7.RPKM.,Late.blastocyst..3..Cell.8.RPKM.
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+2,2,2,2,11,12,11,7,7,7,7,7,7,13,13,13,14,24,22,14,20,22,23,21,21,27,25,25,27,36,30,30,34,30,33,34,36,38,37,39,39,42,38,43,43,45,46,52,45,51,54,51,26,49,57,56,59,57,59,56,60,70,71,62,67,62,71,69,62,72,62,63,70,76,86,86,81,79,78,76,80,82,82,87,88,89,74,74,88,85,90
+3,3,3,3,12,10,12,8,8,8,8,8,11,14,24,23,21,19,16,19,23,23,18,22,22,26,26,26,26,30,36,34,36,33,36,36,35,40,40,40,41,40,40,38,44,49,54,26,51,54,51,50,28,51,50,59,60,53,58,58,53,61,61,63,64,69,66,64,82,70,70,72,81,71,75,75,76,81,76,78,76,81,78,75,80,88,86,86,90,77,81
+4,6,7,6,4,11,4,9,9,9,9,9,12,24,14,16,16,23,18,23,18,24,13,13,13,40,38,40,38,29,29,29,29,29,29,29,29,42,38,38,37,37,42,37,41,51,50,28,48,50,50,53,47,54,53,54,58,60,56,54,50,71,68,82,65,65,68,67,68,67,65,65,72,73,73,80,82,82,79,79,75,76,79,86,73,85,83,87,89,89,85
+5,5,5,5,5,5,5,12,12,12,12,11,5,22,23,15,24,17,21,17,22,18,22,24,23,25,28,28,28,31,31,31,35,36,35,31,31,41,41,41,40,41,41,41,38,53,51,27,50,49,46,46,52,53,51,58,56,51,55,59,51,65,62,71,72,70,72,66,78,65,72,69,65,70,74,74,79,77,82,77,84,72,76,83,75,72,87,75,85,90,89
diff -r 000000000000 -r 5421e01f640a test-data/closest_cells_clusters.rds
Binary file test-data/closest_cells_clusters.rds has changed
diff -r 000000000000 -r 5421e01f640a test-data/closest_cells_similarities.csv
--- /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
@@ -0,0 +1,6 @@
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diff -r 000000000000 -r 5421e01f640a test-data/index_cell.rds
Binary file test-data/index_cell.rds has changed
diff -r 000000000000 -r 5421e01f640a test-data/index_cluster.png
Binary file test-data/index_cluster.png has changed
diff -r 000000000000 -r 5421e01f640a test-data/index_cluster.rds
Binary file test-data/index_cluster.rds has changed
diff -r 000000000000 -r 5421e01f640a test-data/project_cluster.csv
--- /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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