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changeset 1:7bf891a13ace draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 8417888e4ecc1fd033d3412957c5475e29f66403
author iuc
date Sat, 01 Oct 2022 14:11:42 +0000
parents 3fe0d1df3950
children b1ca81ce88f9
files test-data/test_reads.fastqsanger.gz vapor.xml
diffstat 2 files changed, 9 insertions(+), 4 deletions(-) [+]
line wrap: on
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Binary file test-data/test_reads.fastqsanger.gz has changed
--- a/vapor.xml	Wed Aug 24 09:51:46 2022 +0000
+++ b/vapor.xml	Sat Oct 01 14:11:42 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy1" profile="21.05">
     <description>
         Classify Influenza samples from raw short read sequence data
     </description>
@@ -29,7 +29,7 @@
     ]]>    </command>
     <inputs>
         <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
-        <param name="fastq_file" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
+        <param name="fastq_file" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
         <param name="output_type" type="select" label="Output type">
             <option value="scores" selected="true">Return scores only</option>
             <option value="fasta">Return FASTA only</option>
@@ -44,13 +44,13 @@
         </section>
     </inputs>
     <outputs>
-        <data name="output_scores" from_work_dir="out_file" format="tabular" label="VAPOR: closest reference">
+        <data name="output_scores" from_work_dir="out_file" format="tabular" label="${tool.name} on ${on_string}: closest reference scores">
             <filter>output_type == "scores"</filter>
             <actions>
                 <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
             </actions>
         </data>
-        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="VAPOR: closest reference (fasta)">
+        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
             <filter>output_type == "fasta"</filter>
         </data>
     </outputs>
@@ -62,6 +62,11 @@
         </test>
         <test expect_num_outputs="1">
             <param name="fasta_file" value="HA_sample.fa" />
+            <param name="fastq_file" value="test_reads.fastqsanger.gz" />
+            <output name="output_scores" file="output1.tab" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="fasta_file" value="HA_sample.fa" />
             <param name="fastq_file" value="test_reads.fq" />
             <section name="opt">
                 <param name="kmer_length" value="29" />