# HG changeset patch
# User ebi-gxa
# Date 1554307526 14400
# Node ID 040d4b3a19d56203e274362043b670562557311f

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4

diff -r 000000000000 -r 040d4b3a19d5 gtf2gene.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf2gene.R	Wed Apr 03 12:05:26 2019 -0400
@@ -0,0 +1,8 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(require(rtracklayer))
+args <- commandArgs(TRUE)
+
+annotation <- elementMetadata(import( args[1] ))
+genes <- unique(annotation[['gene_id']])
+writeLines(genes[ ! is.na(genes)], con = 'genes.txt')
diff -r 000000000000 -r 040d4b3a19d5 gtf2gene_list.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf2gene_list.xml	Wed Apr 03 12:05:26 2019 -0400
@@ -0,0 +1,54 @@
+<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0">
+    <description>extracts gene ids from Ensembl GTF using rtracklayer</description>
+    <requirements>
+      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+       ln -s '$gtf_input' input.gtf;
+       Rscript $__tool_directory__/gtf2gene.R input.gtf
+	    ]]></command>
+
+    <inputs>
+        <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" />
+    </inputs>
+
+    <outputs>
+        <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/>
+        <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/>
+      </test>
+    </tests>
+
+
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file.
+
+**Inputs**
+
+    * Ensembl GTF file
+
+-----
+
+**Outputs**
+
+    * Gene identifier list in tsv.
+]]></help>
+<citations>
+  <citation type="bibtex">
+@misc{github-hinxton-single-cell,
+author = {Pablo Moreno, EBI Gene Expression Team},
+year = {2019},
+title = {Hinxton Single Cell Anlysis Environment},
+publisher = {GitHub},
+journal = {GitHub repository},
+url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
+  }</citation>
+</citations>
+</tool>