diff plasflow.xml @ 1:ea270d0ad0e6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6

--- a/plasflow.xml	Thu Sep 27 06:41:19 2018 -0400
+++ b/plasflow.xml	Sat Jan 21 13:49:39 2023 +0000
@@ -1,17 +1,29 @@
-<tool id="PlasFlow" name="PlasFlow" version="1.0">
+<tool id="PlasFlow" name="PlasFlow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <description>Prediction of plasmid sequences in metagenomic contigs</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.1.0">plasflow</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">plasflow</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+## PlasFlow supports gz only partially 
+## https://github.com/smaegol/PlasFlow/blob/45604ff637c65f709dabff63e665fa60896be241/PlasFlow.py#L444
+#if $readFile.ext == "fasta.gz"
+    gunzip -c '$readFile' > 'reads.fasta' &&
+#else
+    ln -s '$readFile' 'reads.fasta' &&
+#end if
+
 PlasFlow.py
---input '$readFile'
+--input 'reads.fasta'
 --output 'output'
 --threshold '$threshold'
     ]]></command>
     <inputs>
-        <param name="readFile" type="data" format="fastq,fasta" optional="true" label="Sequence Reads" />
-        <param argument="threshold" type="float" value="0.7" label="Threshold for porbability filtering"/>
+        <param name="readFile" type="data" format="fasta,fasta.gz" optional="true" label="Contig Sequences" />
+        <param argument="threshold" type="float" value="0.7" min="0" max="1" label="Threshold for probability filtering"/>
     </inputs>
     <outputs>
         <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
@@ -21,16 +33,29 @@
     </outputs>
     <tests>
         <test>
-            <param name="readFile" value="test.fasta"/>
+            <param name="readFile" value="test.fasta" ftype="fasta"/>
             <param name="threshold" value="0.7"/>
-            <output name="probability_table" value="output"/>
+            <output name="probability_table" value="output" compare="re_match"/>
+            <output name="chromosomes" value="output_chromosomes.fasta"/>
+            <output name="plasmids" value="output_plasmids.fasta"/>
+            <output name="unclassified" value="output_unclassified.fasta"/>
+        </test>
+        <test>
+            <param name="readFile" value="test.fasta.gz" ftype="fasta.gz"/>
+            <param name="threshold" value="0.7"/>
+            <output name="probability_table" value="output" compare="re_match"/>
             <output name="chromosomes" value="output_chromosomes.fasta"/>
             <output name="plasmids" value="output_plasmids.fasta"/>
             <output name="unclassified" value="output_unclassified.fasta"/>
         </test>
     </tests>
     <help><![CDATA[
-PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. It relies on the neural network models trained on full genome and plasmid sequences and is able to differentiate between plasmids and chromosomes with accuracy reaching 96%. It outperforms other available solutions for plasmids recovery from metagenomes and incorporates the thresholding which allows for exclusion of incertain predictions. PlasFlow has been published in Nucleic Acids Research
+PlasFlow is a set of scripts used for prediction of plasmid sequences in
+metagenomic contigs. It relies on the neural network models trained on full
+genome and plasmid sequences and is able to differentiate between plasmids and
+chromosomes with accuracy reaching 96%. It outperforms other available solutions
+for plasmids recovery from metagenomes and incorporates the thresholding which
+allows for exclusion of incertain predictions.
     ]]></help>
     <citations>
         <citation type="doi">10.1093/nar/gkx1321</citation>