Mercurial > repos > ebi-gxa > scmap_get_std_output

changeset 7:2f63b1cd9122 draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:42:47 +0000
parents 0d713384d8d8
children
files 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
diffstat 14 files changed, 9 insertions(+), 114 deletions(-) [+]
line wrap: on
line diff
--- a/scmap_get_std_output.xml	Thu Aug 13 06:10:49 2020 -0400
+++ b/scmap_get_std_output.xml	Fri Nov 27 13:42:47 2020 +0000
@@ -5,12 +5,15 @@
     </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 "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}"
+        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}"  --tool '${tool}' --sim-col-name "${sim_col_name}"
+        #if $index
+          --index "${index}"
+        #end if   
     ]]></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="data" name="index" label="Scmap index object" format="rdata" help="Scmap index object in rdata format" />
+        <param type="data" name="index" label="Scmap index object" optional="true" format="rdata" help="Scmap index object in rdata format" />
         <param type="select" name="tool" label="Tool used (cell/cluster)"  help="What tool was used - scmap-cell or scmap-cluster?">
             <option value="scmap-cell">Scmap-cell</option>
             <option value="scmap-cluster">Scmap-cluster</option>
@@ -22,7 +25,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_predictions_file" value="project_cluster.csv" />
+            <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
             <param name="include_scores" value="TRUE" />
             <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
         </test>
--- a/scmap_macros.xml	Thu Aug 13 06:10:49 2020 -0400
+++ b/scmap_macros.xml	Fri Nov 27 13:42:47 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.6.2</token>
+    <token name="@TOOL_VERSION@">1.6.3</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="0.0.10">scmap-cli</requirement>
+        <requirement type="package" version="0.0.11">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+1.6.3+galaxy0: Update scmap-cli to 0.0.11
 1.6.2+galaxy0: Update scmap-cli to 0.0.10
 1.6.1+galaxy0: Update scmap-cli to 0.0.9.
 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/.
--- a/test-data/closest_cells.csv	Thu Aug 13 06:10:49 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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--- a/test-data/closest_cells_clusters.csv	Thu Aug 13 06:10:49 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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Binary file test-data/closest_cells_clusters.rds has changed
--- a/test-data/closest_cells_similarities.csv	Thu Aug 13 06:10:49 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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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
--- a/test-data/project_cluster.csv	Thu Aug 13 06:10:49 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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-70,Late.blastocyst..1..Cell.10.RPKM.,blast,0.956481724858848,blast
-71,Late.blastocyst..1..Cell.11.RPKM.,blast,0.956159281369748,blast
-72,Late.blastocyst..1..Cell.12.RPKM.,blast,0.96425809974187,blast
-73,Late.blastocyst..2..Cell.1.RPKM.,blast,0.954566650006314,blast
-74,Late.blastocyst..2..Cell.2.RPKM.,blast,0.859795704593317,blast
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-81,Late.blastocyst..2..Cell.9.RPKM.,blast,0.958716824617989,blast
-82,Late.blastocyst..2..Cell.10.RPKM.,blast,0.966000611704395,blast
-83,Late.blastocyst..3..Cell.1.RPKM.,blast,0.830150497819373,blast
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-88,Late.blastocyst..3..Cell.6.RPKM.,blast,0.923562228265187,blast
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-90,Late.blastocyst..3..Cell.8.RPKM.,blast,0.917408664281774,blast
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