Galaxy |

Changeset 0:cb6b70d45519 (2019-09-16)

Next changeset 1:c2ca3bc40523 (2019-10-25)

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

added:
scmap_macros.xml
scmap_scmap_cell.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

diff -r 000000000000 -r cb6b70d45519 scmap_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_macros.xml Mon Sep 16 09:56:58 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 cb6b70d45519 scmap_scmap_cell.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_scmap_cell.xml Mon Sep 16 09:56:58 2019 -0400

[

@@ -0,0 +1,60 @@
+<tool id="scmap_scmap_cell" name="scmap cell projection" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-scmap-cell.R
+            -i '$index_single_cell_experiment'
+            -p '$project_single_cell_experiment'
+            --number-nearest-neighbours '$n_nearest_neighbours'
+            --cluster-col '${cluster_projection.cluster_col}'
+            --output-object-file '$output_single_cell_experiment'
+            --closest-cells-text-file '$closest_cells_text_file'
+            --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
+            #if $cluster_projection
+            --output-clusters-text-file '$closest_cells_clusters_csv'
+            #end if
+      ]]></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="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" />
+
+     <conditional name="cluster_projection">
+        <param name="cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>
+        <when value="true" >
+          <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." />
+        </when>
+        <when value="false" >
+          <param name="cluster_col" type="hidden" value="NULL" />
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data name="output_single_cell_experiment" format="rdata" />
+      <data name="closest_cells_text_file" format="csv" />
+      <data name="closest_cells_similarities_text_file" format="csv" />
+      <data name="closest_cells_clusters_csv" format="csv">
+        <filter>cluster_projection == "true"</filter>
+      </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
+            <param name="cluster_projection" value="true" ftype="rdata"/>
+            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds"/>
+            <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" />
+            <output name="closest_cells_text_file" file="closest_cells.csv"/>
+            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r cb6b70d45519 test-data/closest_cells.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells.csv Mon Sep 16 09:56:58 2019 -0400

@@ -0,0 +1,6 @@
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diff -r 000000000000 -r cb6b70d45519 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 09:56:58 2019 -0400

diff -r 000000000000 -r cb6b70d45519 test-data/closest_cells_clusters.rds

Binary file test-data/closest_cells_clusters.rds has changed

diff -r 000000000000 -r cb6b70d45519 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 09:56:58 2019 -0400

b'@@ -0,0 +1,6 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diff -r 000000000000 -r cb6b70d45519 test-data/index_cell.rds

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diff -r 000000000000 -r cb6b70d45519 test-data/index_cluster.png

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diff -r 000000000000 -r cb6b70d45519 test-data/index_cluster.rds

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diff -r 000000000000 -r cb6b70d45519 test-data/project_cluster.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.csv Mon Sep 16 09:56:58 2019 -0400

@@ -0,0 +1,91 @@
+,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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diff -r 000000000000 -r cb6b70d45519 test-data/project_cluster.rds

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diff -r 000000000000 -r cb6b70d45519 test-data/select_features.png

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diff -r 000000000000 -r cb6b70d45519 test-data/select_features.rds

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diff -r 000000000000 -r cb6b70d45519 test-data/test_sce.rds

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