changeset 0:e72652c6edb9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emmtyper.xml	Fri Mar 31 17:14:38 2023 +0000
@@ -0,0 +1,76 @@
+l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0">
+    <requirements>
+        <requirement type="package">emmtyper</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        emmtyper -o '$output1' '$input1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fasta" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" from_work_dir="results.txt" />
+    </outputs>
+    <help><![CDATA[
+        Usage: emmtyper [OPTIONS] [FASTA]...
+
+  Welcome to emmtyper.
+
+  Usage:
+
+  emmtyper *.fasta
+
+Options:
+  --version                       Show the version and exit.
+  -w, --workflow [blast|pcr]      Choose workflow  [default: blast]
+  -d, --blast_db TEXT             Path to EMM BLAST DB
+  -k, --keep                      Keep BLAST and isPcr output files.
+  -d, --cluster-distance INTEGER  Distance between cluster of matches to
+                                  consider as different clusters.  [default:
+                                  500]
+  -o, --output TEXT               Output stream. Path to file for output to a
+                                  file.  [default: stdout]
+  -f, --output-format [short|verbose|visual]
+                                  Output format.
+  --dust [yes|no|level window linker]
+                                  [BLAST] Filter query sequence with DUST.
+                                  [default: no]
+  --percent-identity INTEGER      [BLAST] Minimal percent identity of
+                                  sequence.  [default: 95]
+  --culling-limit INTEGER         [BLAST] Total hits to return in a position.
+                                  [default: 5]
+  --mismatch INTEGER              [BLAST] Threshold for number of mismatch to
+                                  allow in BLAST hit.  [default: 4]
+  --align-diff INTEGER            [BLAST] Threshold for difference between
+                                  alignment length and subject length in BLAST
+                                  hit.  [default: 5]
+  --gap INTEGER                   [BLAST] Threshold gap to allow in BLAST hit.
+                                  [default: 2]
+  --blast-path TEXT               [BLAST] Specify full path to blastn
+                                  executable.
+  --primer-db TEXT                [isPcr] PCR primer. Text file with 3
+                                  columns: Name, Forward Primer, Reverse
+                                  Primer. 
+  --min-perfect INTEGER           [isPcr] Minimum size of perfect match at 3'
+                                  primer end.  [default: 15]
+  --min-good INTEGER              [isPcr] Minimum size where there must be 2
+                                  matches for each mismatch.  [default: 15]
+  --max-size INTEGER              [isPcr] Maximum size of PCR product.
+                                  [default: 2000]
+  --ispcr-path TEXT               [isPcr] Specify full path to isPcr
+                                  executable.
+  --help                          Show this message and exit.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubemmtyper,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {emmtyper},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/MDU-PHL/emmtyper},
+}</citation>
+    </citations>
+</tool>