Mercurial > repos > iuc > tximport

diff tximport.xml @ 1:2c338211927c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
author iuc
date Thu, 23 Sep 2021 00:18:22 +0000
parents 206a71a69161
children 1906cb429215
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line diff
--- a/tximport.xml	Wed Dec 04 05:57:26 2019 -0500
+++ b/tximport.xml	Thu Sep 23 00:18:22 2021 +0000
@@ -1,9 +1,15 @@
-<tool id="tximport" name="tximport" version="0.1">
+<tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09">
+    <macros>
+        <token name="@TOOL_VERSION@">1.20.0</token>
+    </macros>
     <description>Summarize transcript-level estimates for gene-level analysis</description>
+    <xrefs>
+        <xref type="bio.tools">tximport</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="1.20.2">r-getopt</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement>
+        <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="1.20.3">r-getopt</requirement>
     </requirements>
 
     <stdio>
@@ -123,9 +129,9 @@
         </conditional>
         <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?">
             <option value="no">No</option>
-            <option value="scaled_TPM">Scaled up to library size</option>
-            <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option>
-            <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
+            <option value="scaledTPM">Scaled up to library size</option>
+            <option value="lengthScaledTPM">Scaled using the avg. transcript legth over samples and then the library size</option>
+            <option value="dtuScaledTPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
         </param>
     </inputs>
     <outputs>