diff xpore_dataprep.xml @ 0:b64b9a2bf4f0 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xpore_dataprep.xml	Wed May 26 23:14:24 2021 +0000
@@ -0,0 +1,87 @@
+<tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1">
+  <description></description>
+  <requirements>
+        <requirement type="package" version="0.5.6">xpore</requirement>
+        <requirement type="package" version="1.9.0">pyensembl</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+        xpore-dataprep
+            --eventalign '$eventalign_reads'
+            --summary '$eventalign_summary'
+            --out_dir out
+            --n_processes \${GALAXY_SLOTS:-4} &&
+            ls -la out
+  ]]></command>
+ <inputs>
+    <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
+           help="a nanopolish eventalign output that aligns the nanopore events to a reference" />
+    <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary"
+           help="a summary of nanopolish eventalign by read_name,read_index" />
+ </inputs>
+
+ <outputs>
+    <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" />
+    <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" />
+    <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" />
+    <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" />
+    <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" />
+    <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/>
+</outputs>
+
+<tests>
+    <test>
+        <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" />
+        <param name="eventalign_summary" value="dataprep_eventaligh_summary.tsv" ftype="tabular" />
+        <output file="data.index" name="data_index" />
+        <output file="data.log" name="data_log" />
+        <output file="eventalign.log" name="eventalign_log" />
+        <output file="data.readcount" name="data_readcount" />
+        <output file="data.json" name="data_json" />
+        <output file="eventalign.hdf5" name="eventalign_hdf5" compare="sim_size" delta="3000" />
+    </test>
+</tests>
+<help>
+
+**What it does**
+
+Prepare data for differential analysis by xpore-diffmod analysis of differential RNA
+modification across all tested positions.
+
+.. class:: warningmark
+
+In its current version, only preparation of data for analysis by xpore-diffmod based on a
+**transcripts** collection reference is implemented.
+
+**Inputs**
+
+This tools requires the following inputs::
+
+- the "aligned nanopore events" file returned from nanopolish eventalign (also named squiggles)
+- the "nanopolish summary" file also returned by nanopolish eventalign
+
+**Outputs**
+
+3 datasets that will be required by xpore-diffmod::
+
+- data.index
+- data.json
+- data.readcount
+
+plus 3 datasets not required by xpore-diffmod::
+
+- data.log
+- eventalign.hdf5
+- eventalign.log
+
+for details on xpore-data prep, see https://xpore.readthedocs.io/en/latest/index.html
+and https://github.com/GoekeLab/xpore
+
+</help>
+
+<citations>
+    <citation type="doi">10.1101/2020.06.18.160010</citation>
+</citations>
+</tool>