Mercurial > repos > greg > vsnp_statistics

diff vsnp_statistics.xml @ 5:d0fbdeaaa488 draft

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
author greg
date Wed, 16 Jun 2021 17:38:47 +0000
parents 2d6c6b01319e
children de2af65c4633
line wrap: on
line diff
--- a/vsnp_statistics.xml	Sun Jan 03 15:47:28 2021 +0000
+++ b/vsnp_statistics.xml	Wed Jun 16 17:38:47 2021 +0000
@@ -4,10 +4,10 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
+        <requirement type="package" version="1.78">biopython</requirement>
         <requirement type="package" version="1.16.5">numpy</requirement>
         <requirement type="package" version="0.25.3">pandas</requirement>
         <requirement type="package" version="1.2.0">xlrd</requirement>
-        <requirement type="package" version="1.2.8">xlsxwriter</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import re
@@ -121,7 +121,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output" format="xlsx"/>
+        <data name="output" format="tabular"/>
     </outputs>
     <tests>
         <!-- A single fastq file -->
@@ -131,7 +131,7 @@
             <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
             <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/>
             <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/>
-            <output name="output" file="vsnp_statistics1.xlsx" ftype="xlsx" compare="sim_size"/>
+            <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/>
         </test>
         <!-- A set of paired fastq files -->
         <test expect_num_outputs="1">
@@ -141,7 +141,7 @@
             <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
             <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/>
             <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/>
-            <output name="output" file="vsnp_statistics2.xlsx" ftype="xlsx" compare="sim_size"/>
+            <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/>
         </test>
         <!-- A collection of SE fastq files -->
         <test expect_num_outputs="1">
@@ -165,7 +165,7 @@
                     <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/>
                 </collection>
             </param>
-            <output name="output" file="vsnp_statistics3.xlsx" ftype="xlsx" compare="sim_size"/>
+            <output name="output" file="vsnp_statistics3.tabular" ftype="tabular"/>
         </test>
         <!-- A collection of PE fastq files -->
         <test expect_num_outputs="1">
@@ -187,7 +187,7 @@
                     <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/>
                 </collection>
             </param>
-            <output name="output" file="vsnp_statistics4.xlsx" ftype="xlsx" compare="sim_size"/>
+            <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/>
         </test>
     </tests>
     <help>