Repository 'scmap_select_features'
hg clone https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_select_features

Changeset 0:22b605f49f5f (2019-09-16)
Next changeset 1:953c7ff4069e (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_select_features.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
b
diff -r 000000000000 -r 22b605f49f5f scmap_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_macros.xml Mon Sep 16 09:57:48 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" $(R --vanilla --slave -e "library(scmap); cat(sessionInfo()\$otherPkgs\$scmap\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @Article{,
+            title = {scmap - A tool for unsupervised projection of single cell RNA-seq data},
+            author = {Vladimir Yu. Kiselev and Martin Hemberg},
+            year = {2017},
+            journal = {bioRxiv},
+            url = {http://doi.org/10.1101/150292},
+          }
+        </citation>
+        <citation type="bibtex">
+          @misc{githubscmap-cli.git,
+            author = {Jonathan Manning, EBI Gene Expression Team},
+            year = {2018},
+            title = {scmap-cli: command line interface for scmap},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/scmap-cli.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
b
diff -r 000000000000 -r 22b605f49f5f scmap_select_features.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_select_features.xml Mon Sep 16 09:57:48 2019 -0400
[
@@ -0,0 +1,31 @@
+<tool id="scmap_select_features" name="scmap select features" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <description>finds the most informative features (genes/transcripts) for projection.</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-select-features.R --input-object-file '$input_single_cell_experiment' --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />
+        <param name="n_features" type="integer" label="Number of features" value="500" help="Number of features to be selected" />
+    </inputs>
+    <outputs>
+        <data name="output_single_cell_experiment" format="rdata" />
+        <data name="plot" format="png" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
+            <output name="output_single_cell_experiment" file="select_features.rds"/>
+            <output name="plot" file="select_features.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
b
diff -r 000000000000 -r 22b605f49f5f test-data/closest_cells.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells.csv Mon Sep 16 09:57:48 2019 -0400
b
@@ -0,0 +1,6 @@
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b
diff -r 000000000000 -r 22b605f49f5f 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 09:57:48 2019 -0400
b
@@ -0,0 +1,6 @@
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b
diff -r 000000000000 -r 22b605f49f5f test-data/closest_cells_clusters.rds
b
Binary file test-data/closest_cells_clusters.rds has changed
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diff -r 000000000000 -r 22b605f49f5f 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 09:57:48 2019 -0400
b
b'@@ -0,0 +1,6 @@\n+,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.\n+1,0.974273699811975,0.973659311436167,0.974854220234444,0.97839753346497,0.979490174962032,0.980115537598401,0.976313835558767,0.976881116973313,0.975901392182175,0.977322845448825,0.976323350516014,0.976971559860292,0.976320366157395,0.969912061538871,0.968501468487668,0.971522498841011,0.964951572472287,0.972748756493633,0.971942905027406,0.972017001342311,0.980520343865064,0.978080837270881,0.980078705456514,0.979798181564745,0.966241474136935,0.969158473501728,0.968707192268454,0.969841095031548,0.974854612410912,0.976503242175562,0.979804630823918,0.976544473170974,0.969481019998013,0.976489477308787,0.979995497607925,0.979854110006233,0.981867832635268,0.974786591856287,0.973765988696476,0.977837020195143,0.982102656773436,0.970638900011281,0.974968488962187,0.969481110283021,0.950812756659853,0.96807907709823,0.91630840568286,0.970572967922616,0.969146983045072,0.963005588968003,0.972427039750112,0.726218083982927,0.969017360461502,0.974170553961338,0.964279804847546,0.957081439198935,0.956990695530537,0.947526173473035,0.961646669180513,0.963312355197477,0.929414192606584,0.945349776265469,0.931894436659203,0.928302728076479,0.93495880629305,0.928964466633903,0.935785405180646,0.946332771937332,0.944210967521674,0.935446129048361,0.957020095156881,0.936513899155052,0.941244285216586,'..b'549,0.970520527970828,0.968478100687963,0.964493691190741,0.972285524744667,0.724424734546886,0.969559396842649,0.969364813048294,0.958239742574716,0.944755601653579,0.959029210899153,0.968964013352534,0.963723725469498,0.960711969960917,0.949879991563679,0.942457767725231,0.950427652531018,0.948091129226388,0.935725154213454,0.947068372664074,0.932792955705649,0.939589564737004,0.929847717771756,0.950599081967672,0.940231698364827,0.939390494922626,0.938175389389597,0.892258057827176,0.926372907311768,0.95245650968153,0.922841768364733,0.937416110024372,0.933878349854862,0.878774403798334,0.944167607789112,0.9386829330418,0.830037046627661,0.883713143953103,0.928636951069851,0.91354245801598,0.86465693599049,0.905142929288076,0.911070328984465,0.90368380440602\n+4,0.969539415685062,0.968605789622234,0.969975869820421,0.978880784666248,0.979406018332084,0.979819636687998,0.976293636860104,0.976907817743082,0.975961272994989,0.977298240230832,0.976152456170403,0.977158123689469,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diff -r 000000000000 -r 22b605f49f5f test-data/index_cluster.png
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diff -r 000000000000 -r 22b605f49f5f test-data/index_cluster.rds
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diff -r 000000000000 -r 22b605f49f5f test-data/project_cluster.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.csv Mon Sep 16 09:57:48 2019 -0400
b
@@ -0,0 +1,91 @@
+,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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