changeset 0:0ff5b94932fe draft

"planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"

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+++ b/README.md	Tue May 31 10:56:52 2022 +0000
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+# get_Organelle_galaxy_wraper
+
+this repository provide getOrganelle tool for Galaxy server. As dependency it used reference database https://github.com/Kinggerm/GetOrganelleDB. The copy of database is installed from repositories https://github.com/kavonrtep/getorganelledb and this dependency is defined in https://github.com/kavonrtep/package_getorganelledb_0_0_1.
+
+Package can be installed from Galaxy toolshed.
+
+List of components:
+- tool definition: this repository 
+  - source - this repository
+  - toolshed - .......
+- dependency package:
+  - source https://github.com/kavonrtep/package_getorganelledb_0_0_1
+  - toolshed package
+- database location - https://github.com/kavonrtep/getorganelledb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_organelle.xml	Tue May 31 10:56:52 2022 +0000
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+<tool id="get_organelle" name="Assemble organelle genome from genomic skimming data" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="1.7.6.1">getOrganelle</requirement>
+        <requirement type="package" version="0.0.1">getorganelledb</requirement>
+        <requirement type="set_environment">GETORGANELLEDB</requirement>
+
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} &&
+        cat assembly_dir/*.fasta > ${assembly_contigs} &&
+        zip -r assembly.zip assembly_dir &&
+        mv assembly.zip ${assembly_zip}
+
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/>
+        <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" />
+        <param type="select" label="Assembly type" name="ref_db" >
+            <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option>
+            <option value="embplant_mt">Embryophyta plant mitogenome </option>
+            <option value="embplant_nr">Embryophyta plant ribosomal RNA </option>
+            <option value="other_pt">Non-embryophyta plant plastome </option>
+            <option value="animal_mt">Animal mitogenome </option>
+            <option value="fungus_mt">Fungus mitogenome </option>
+            <option value="fungus_nr">Fungus ribosomal RNA </option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" />
+        <data name="assembly_zip" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" />
+    </outputs>
+    <help><![CDATA[
+        This toolkit assemblies organelle genome from genomic skimming data.
+
+        Citation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241 (2020). https://doi.org/10.1186/s13059-020-02154-5
+
+        Source code - https://github.com/Kinggerm/GetOrganelle
+
+        Organelle Database -  https://github.com/Kinggerm/GetOrganelleDB
+
+    ]]></help>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 31 10:56:52 2022 +0000
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+<?xml version="1.0" ?>
+<tool_dependency>
+    <package name="getorganelledb" version="0.0.1">
+        <repository name="package_getorganeledb_0_0_1" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="4667f2fed156"/>
+        <readme>
+      getorganelle reference database
+    </readme>
+    </package>
+</tool_dependency>