changeset 1:b304c1ffe80c draft

Deleted selected files

--- a/lissero.xml	Sat Nov 19 21:36:05 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="lissero" name="Serogrouping typing prediction for Listeria monocytogenes" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <requirements>
-        <requirement type="package">lissero</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        lissero 
-        #if $advanced
-          --min_id $advanced.min_id
-          --min_cov $advanced.min_cov
-        #end_if_
-        '$input1' > '$output1'
-    ]]></command>
-    <inputs>
-        <param type="data" name="input1" format="fasta" />
-        <conditional name="settings">
-            <param name="advanced" type="select" label="Specify advanced parameters">
-                <option value="simple" selected="true">No, use program defaults.</option>
-                <option value="advanced">Yes, see full parameter list.</option>
-            </param>
-            <when value="simple">
-            </when>
-            <when value="advanced">
-                <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" /> 
-                <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" /> 
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="txt" />
-    </outputs>
-    <help><![CDATA[
-        Usage: lissero [OPTIONS] FASTA...
-
-  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
-  lmo0737, ORF2819, ORF2110, Prs
-
-  References:
-
-  * Doumith et al. Differentiation of the major Listeria monocytogenes
-  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
-
-Options:
-  -h, --help              Show this message and exit.
-  -s, --serotype_db TEXT  [default:
-                          /home/strain_remote/miniconda3/lib/python3.9/site-
-                          packages/lissero/db]
-  --min_id FLOAT          Minimum percent identity to accept a match. [0-100]
-                          [default: 95.0]
-  --min_cov FLOAT         Minimum coverage of the gene to accept a match.
-                          [0-100]  [default: 95.0]
-  --debug
-  --logfile TEXT          Save log to a file instead of printing to stderr
-  --version               Show Version Information
-
-    ]]></help>
-    <citations>
-        <citation type="bibtex">
-@misc{githublissero,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {lissero},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/MDU-PHL/lissero},
-}</citation>
-    </citations>
-</tool>