Mercurial > repos > ebi-gxa > scmap_preprocess_sce

changeset 0:a74497e18277 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
author ebi-gxa
date Wed, 29 Apr 2020 12:39:06 -0400
parents
children 559b9d22f264
files scmap_macros.xml scmap_preprocess_sce.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, 176 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_macros.xml	Wed Apr 29 12:39:06 2020 -0400
@@ -0,0 +1,45 @@
+<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>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.8">scmap-cli</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", scmap version" $(R --vanilla --slave -e "library(scmap); cat(sessionInfo()\$otherPkgs\$scmap\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @Article{,
+            title = {scmap - A tool for unsupervised projection of single cell RNA-seq data},
+            author = {Vladimir Yu. Kiselev and Martin Hemberg},
+            year = {2017},
+            journal = {bioRxiv},
+            url = {http://doi.org/10.1101/150292},
+          }
+        </citation>
+        <citation type="bibtex">
+          @misc{githubscmap-cli.git,
+            author = {Jonathan Manning, EBI Gene Expression Team},
+            year = {2018},
+            title = {scmap-cli: command line interface for scmap},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/scmap-cli.git},
+          }
+        </citation>
+        <citation type="doi">10.1101/2020.04.08.032698</citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_preprocess_sce.xml	Wed Apr 29 12:39:06 2020 -0400
@@ -0,0 +1,22 @@
+<tool id="scmap_preprocess_sce" name="Scmap pre-process" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Pre-process SCE object before running downstream analysis</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${output_single_cell_experiment}"
+        ]]></command>
+    <inputs>
+        <param type="data" name="input_single_cell_experiment" label="Input SCE object" format="rdata" help="SCE object to be pre-processed" />
+    </inputs>
+    <outputs>
+        <data name="output_single_cell_experiment" format="rdata" />
+    </outputs>
+    <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	Wed Apr 29 12:39:06 2020 -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	Wed Apr 29 12:39:06 2020 -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	Wed Apr 29 12:39:06 2020 -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	Wed Apr 29 12:39:06 2020 -0400
@@ -0,0 +1,91 @@
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