Galaxy |

Changeset 0:5f95950c3959 (2020-04-03)

Next changeset 1:656c588b718c (2020-04-24)

Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"

added:
scmap_get_std_output.xml
scmap_macros.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 5f95950c3959 scmap_get_std_output.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_get_std_output.xml Fri Apr 03 06:33:57 2020 -0400

[

@@ -0,0 +1,38 @@
+<tool id="scmap_get_std_output" name="scmap get standard output" version="@TOOL_VERSION@+galaxy1"  profile="@PROFILE@">
+    <description>Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
+    <macros>
+         <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --sim-col-name "${sim_col_name}"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
+        <param type="boolean" name="include_scores" checked="false"  label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" />
+        <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
+    </inputs>
+    <outputs>
+        <data name="output_predictions_file" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_predictions_file" value="project_cluster.csv" />
+            <param name="include_scores" value="TRUE" />
+            <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis.
+    See the example snippet below:
+    ________________________________________
+    |  cell_id   | predicted_label | score |
+    | ERR2632411 | memory B cell   |  0.8  |
+    ...
+
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+

diff -r 000000000000 -r 5f95950c3959 scmap_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_macros.xml Fri Apr 03 06:33:57 2020 -0400

[

@@ -0,0 +1,44 @@
+<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="0.0.5">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 5f95950c3959 test-data/closest_cells.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells.csv Fri Apr 03 06:33:57 2020 -0400

@@ -0,0 +1,6 @@
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diff -r 000000000000 -r 5f95950c3959 test-data/closest_cells_clusters.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_clusters.csv Fri Apr 03 06:33:57 2020 -0400

diff -r 000000000000 -r 5f95950c3959 test-data/closest_cells_clusters.rds

Binary file test-data/closest_cells_clusters.rds has changed

diff -r 000000000000 -r 5f95950c3959 test-data/closest_cells_similarities.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_similarities.csv Fri Apr 03 06:33:57 2020 -0400

b'@@ -0,0 +1,6 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diff -r 000000000000 -r 5f95950c3959 test-data/index_cell.rds

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diff -r 000000000000 -r 5f95950c3959 test-data/index_cluster.png

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diff -r 000000000000 -r 5f95950c3959 test-data/index_cluster.rds

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diff -r 000000000000 -r 5f95950c3959 test-data/project_cluster.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.csv Fri Apr 03 06:33:57 2020 -0400

@@ -0,0 +1,91 @@
+,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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diff -r 000000000000 -r 5f95950c3959 test-data/project_cluster.rds

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diff -r 000000000000 -r 5f95950c3959 test-data/select_features.png

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diff -r 000000000000 -r 5f95950c3959 test-data/select_features.rds

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diff -r 000000000000 -r 5f95950c3959 test-data/test_sce.rds

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