Mercurial > repos > eschen42 > mqppep_preproc

diff mqppep_preproc.xml @ 5:b91809a18dbe draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
author eschen42
date Thu, 10 Mar 2022 23:43:38 +0000
parents 8be24b489992
children 36f183e5e4ed
line wrap: on
line diff
--- a/mqppep_preproc.xml	Mon Mar 07 20:43:23 2022 +0000
+++ b/mqppep_preproc.xml	Thu Mar 10 23:43:38 2022 +0000
@@ -53,7 +53,7 @@
       ) && (
         echo '--- kinase-mapping step:'
       ) && (
-        perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
+        \$CONDA_PREFIX/bin/perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
         -i '$phosphoPepIntensities'
         -f '$protein_fasta'
         -n '$networkin'
@@ -338,7 +338,7 @@
 **Input databases**
 
 ``networkin``
-  This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0.  The ENSEMBL data used to generate the file were from Ensembl, `https://ensembl.org <https://ensembl.org>`_ [Howe 2021].
+    This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0.  The ENSEMBL data used to generate the file were from Ensembl, `ensembl.org <https://web.archive.org/web/20220308011159/http://useast.ensembl.org/index.html>`_ [Howe 2021].
 
        *To generate this file:*