Mercurial > repos > iuc > tbprofiler

diff tb_profiler_profile.xml @ 3:19793eecc9f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
author iuc
date Fri, 16 Aug 2019 16:26:31 -0400
parents 49b819f88c2b
children c2656b729ee9
line wrap: on
line diff
--- a/tb_profiler_profile.xml	Tue Jul 16 08:29:18 2019 -0400
+++ b/tb_profiler_profile.xml	Fri Aug 16 16:26:31 2019 -0400
@@ -1,7 +1,10 @@
-<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4">
+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0">
     <description>Infer strain types and drug resistance markers from sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.4">tb-profiler</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
@@ -42,6 +45,8 @@
             --min_gene_frac '${advanced.min_gene_frac}'
             --mapper '${advanced.mapper}'
             --min_depth '${advanced.min_depth}'
+            --af '${min_allel_freq}'
+            --reporting_af '${min_allel_freq_reporting}'
         #end if
 
         #if $output_format == "pdf"
@@ -113,6 +118,8 @@
                     <option value="bowtie2">bowtie2</option>
                 </param>
                 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
+                <param name="min_allel_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
+                <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/>
             </when>
         </conditional>
     </inputs>