Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_build_cell_ontology_dict.xml	Wed Apr 08 15:33:00 2020 +0000
@@ -0,0 +1,38 @@
+<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Create a mapping from labels to CL terms</description>
+    <macros>
+        <import>ct_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p input_dir;
+        #for $sdrf in $input_sdrfs:
+            cp '$sdrf' input_dir/;
+        #end for
+
+        build_cell_ontology_dict.R --input-dir input_dir --condensed-sdrf "${condensed_sdrf}" --barcode-col-name "${barcode_col_name}" --cell-label-col-name "${cell_label_col_name}" --cell-ontology-col-name "${cell_ontology_col_name}" --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}" ]]></command>
+    <inputs>
+        <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="tsv" help="Input SDRF tables" />
+        <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
+        <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files" />
+        <param type="text" name="cell_label_col_name" label="Cell label column name" value="cell.type" help="Name of the cell label field name in provided SDRF files" />
+        <param type="text" name="cell_ontology_col_name" label="Cell ontology column name" value="cell.type.ontology" help="Name of the cell ontology terms column in SDRF files (must be identical across all files)" />
+    </inputs>
+    <outputs>
+        <data name="output_dict_path" format="rdata" />
+        <data name="output_txt_path" format="tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
+            <param name="condensed_sdrf" value="TRUE" />
+            <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_macros.xml	Wed Apr 08 15:33:00 2020 +0000
@@ -0,0 +1,35 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.8">cell-types-analysis</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9]
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+0.0.5+galaxy0: Initial contribution. Andrey Solovyev, 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">
+          @misc{github-cell-types-analysis.git,
+            author = {Andrey Solovyev, EBI Gene Expression Team},
+            year = {2020},
+            title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
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