# HG changeset patch
# User ufz
# Date 1744796600 0
# Node ID 9758bed53a386b01628e60e523e83b07ab08f6be
# Parent  14307de7bbabdef3a89e79a52d997192aa52eb1f
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd

diff -r 14307de7bbab -r 9758bed53a38 end_to_end.xml
--- a/end_to_end.xml	Tue Nov 12 09:31:26 2024 +0000
+++ b/end_to_end.xml	Wed Apr 16 09:43:20 2025 +0000
@@ -37,12 +37,26 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="dbdir" value="phaboxdb"/>
-            <param name="contigs" value="example_contigs.fa"/>
+            <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
             <output name="end_to_end_out">
                 <assert_contents>
-                    <has_n_lines n="11"/>
-                    <has_n_columns n="17"/>
-                    <has_text text="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence&#9;Lineage&#9;PhaGCNScore&#9;Genus&#9;GenusCluster&#9;TYPE&#9;PhaTYPScore&#9;Host&#9;CHERRYScore&#9;Method&#9;Host_NCBI_lineage&#9;Host_GTDB_lineage"/>
+                    <has_n_lines n="391"/>
+                    <has_n_columns n="18"/>
+                    <has_text text="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence&#9;Lineage&#9;PhaGCNScore&#9;Genus&#9;GenusCluster&#9;Prokaryotic virus (Bacteriophages and Archaeal virus)&#9;TYPE&#9;PhaTYPScore&#9;Host&#9;CHERRYScore&#9;Method&#9;Host_NCBI_lineage&#9;Host_GTDB_lineage"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="dbdir" value="phaboxdb"/>
+            <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
+            <section name="phamer">
+                <param name="reject" value="0.1"/>
+            </section>
+            <output name="end_to_end_out">
+                <assert_contents>
+                    <has_n_lines n="391"/>
+                    <has_n_columns n="18"/>
+                    <has_text text="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence&#9;Lineage&#9;PhaGCNScore&#9;Genus&#9;GenusCluster&#9;Prokaryotic virus (Bacteriophages and Archaeal virus)&#9;TYPE&#9;PhaTYPScore&#9;Host&#9;CHERRYScore&#9;Method&#9;Host_NCBI_lineage&#9;Host_GTDB_lineage"/>
                 </assert_contents>
             </output>
         </test>
diff -r 14307de7bbab -r 9758bed53a38 macros.xml
--- a/macros.xml	Tue Nov 12 09:31:26 2024 +0000
+++ b/macros.xml	Wed Apr 16 09:43:20 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.1.5</token>
+    <token name="@TOOL_VERSION@">2.1.11</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="citations">
         <citations>
@@ -44,7 +44,7 @@
             <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/>
             <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/>
             <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/>
-            <!-- \-\-draw not recommended top be used according to CLI help -->
+            <!-- \-\-draw not recommended to be used according to CLI help -->
         </section>
     </xml>
     <token name="@NETWORK@"><![CDATA[
@@ -55,13 +55,15 @@
 
     <xml name="crispr">
         <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help="">
-            <param argument="--bfolder" type="data" format="true" optional="true" label="MAGS"/>
+            <param argument="--bfolder" type="data" format="fasta" optional="true" label="MAGS"/>
+            <param argument="--prophage" type="integer" value="1000" min="0" max="100000" label="Minimum alignment length for estimate potential prophage"/>
             <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/>
             <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/>
             <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program">
                 <option value="blastn">blastn</option>
                 <option value="blastn-short">blastn-short</option>
             </param>
+            <param argument="--magonly" type="boolean" truevalue="--magonly Y" falsevalue="--magonly N" label="Only predicting host based on the provided MAGs" help="Default is to predict the host based on the MAGs and the reference database"/>
         </section>
     </xml>
     <token name="@CRISPR_PRE@"><![CDATA[
@@ -77,9 +79,11 @@
         #if $crispr.bfolder
             --bfolder bfolder
         #end if
+            --prophage $crispr.prophage
             --cpident $crispr.cpident
-            --ccov $crispr.cpident
+            --ccov $crispr.ccov
             --blast $crispr.blast
+            $magonly
     ]]></token>
 
     <xml name="contamination">
@@ -181,6 +185,7 @@
 - PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the ';'.
 - Genus: whether the contig has a genus level name ('-' means unknown).
 - GenusCluster: if the Genus is '-', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences.
+- Prokaryotic virus (Bacteriophages and Archaeal virus): Y/N
     ]]></token>
     <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[
 - TYPE: virulent or temperate (virus).