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changeset 0:b97ecda36fc4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/psortb commit 9275472791234aa6df4ed6e0e533bd9d74d83bdd
author bgruening
date Thu, 18 Dec 2025 16:15:09 +0000
parents
children
files psortb.xml test-data/psortb_arch.fa test-data/psortb_neg.fa test-data/psortb_pos.fa test-data/psortb_pos_output.txt
diffstat 5 files changed, 143 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/psortb.xml	Thu Dec 18 16:15:09 2025 +0000
@@ -0,0 +1,115 @@
+<tool id="psortb" name="PSORTb" version="3.0.6" profile="24.0">
+	<description>Protein subcellular localization prediction for prokaryotes</description>
+    <xrefs>
+        <xref type="bio.tools">psortb</xref>
+    </xrefs>
+    <requirements>
+		<container type="docker">quay.io/galaxy/psortb-cli:3.0.6</container>
+	</requirements>
+	<command detect_errors="exit_code">
+		<![CDATA[
+        mkdir \$TMPDIR/results &&
+		/usr/local/psortb/bin/psort
+        $gram.gram_choice
+		#if $cutoff
+			-c $cutoff
+		#end if
+		#if $divergent
+			-d $divergent
+		#end if
+		-f fasta
+        $exact
+		-o $output_format
+		-i $input_fasta
+		&&
+		mv \$TMPDIR/results/*_psortb_*.txt $output
+		]]>
+	</command>
+
+	<inputs>
+		<param name="input_fasta" type="data" format="fasta" label="Protein sequences (FASTA)" help="Submit protein sequences in FASTA format."/>
+
+		<section name="gram" title="Organism classification" expanded="true">
+			<param name="gram_choice" type="select" label="Organism type">
+				<option value="--positive" selected="true">Gram-positive (Bacteria)</option>
+				<option value="--negative">Gram-negative (Bacteria)</option>
+				<option value="--archaea">Archaea</option>
+			</param>
+		</section>
+
+		<param name="output_format" type="select" label="Output format" help="Choose PSORTb output format.">
+			<option value="normal">Normal (human-readable)</option>
+			<option value="terse">3-column (terse)</option>
+			<option value="long" selected="true">30-column (long)</option>
+		</param>
+        <param argument="--exact" type="boolean" truevalue="--exact" falsevalue="" checked="false" label="Skip SCLBLASTe" help="Useful for batch runs of data against itself in SCLBLAST"/>
+		<param argument="--cutoff" type="float" optional="true" label="Prediction cutoff" help="Sets a cutoff value for reported results (default: 7.5 used internally)."/>
+		<param argument="--divergent" type="float" optional="true" label="Multiple localization cutoff" help="Sets a cutoff for flagging potential multiple localization sites."/>
+	</inputs>
+
+	<outputs>
+		<data name="output" format="txt" label="PSORTb results on ${on_string}"/>
+	</outputs>
+
+	<tests>
+		<test expect_num_outputs="1">
+			<param name="input_fasta" value="psortb_pos.fa"/>
+			<param name="gram|gram_choice" value="--positive"/>
+			<param name="output_format" value="normal"/>
+			<output name="output" value="psortb_pos_output.txt"/>
+		</test>
+		<test expect_num_outputs="1">
+			<param name="input_fasta" value="psortb_neg.fa"/>
+			<param name="gram|gram_choice" value="--negative"/>
+			<param name="output_format" value="terse"/>
+			<output name="output">
+                <assert_contents>
+					<has_text_matching expression="SeqID\tLocalization\tScore" />
+					<has_text_matching expression="NP_949347\.1 \tUnknown\t7\.0" />
+                </assert_contents>
+            </output>
+		</test>
+		<test expect_num_outputs="1">
+			<param name="input_fasta" value="psortb_arch.fa"/>
+			<param name="gram|gram_choice" value="--archaea"/>
+			<param name="output_format" value="long"/>
+            <output name="output">
+				<assert_contents>
+                    <has_text_matching expression="SeqID\s+CMSVM_a_Localization\s+CMSVM_a_Details\s+CWSVM_a_Localization\s+CWSVM_a_Details\s+CytoSVM_a_Localization\s+CytoSVM_a_Details\s+ECSVM_a_Localization\s+ECSVM_a_Details\s+ModHMM_a_Localization\s+ModHMM_a_Details\s+Motif_a_Localization\s+Motif_a_Details\s+Profile_a_Localization\s+Profile_a_Details\s+SCL-BLAST_a_Localization\s+SCL-BLAST_a_Details\s+SCL-BLASTe_a_Localization\s+SCL-BLASTe_a_Details\s+Signal_a_Localization\s+Signal_a_Details\s+Cytoplasmic_Score\s+CytoplasmicMembrane_Score\s+Cellwall_Score\s+Extracellular_Score\s+Final_Localization\s+Final_Localization_Details\s+Final_Score\s+Secondary_Localization\s+PSortb_Version" />
+                    <has_text_matching expression="YP_001689002\.1\s+Unknown\s+Unknown\s+Unknown\s+Extracellular\s+Unknown\s+1 internal helix found\s+Unknown\s+No motifs found\s+Unknown\s+No matches to profiles found\s+Extracellular\s+matched 47117675: Flagellin B1 precursor\s+Unknown\s+No matches against database\s+Unknown\s+No signal peptide detected\s+0.01\s+0.00\s+0.02\s+9.97\s+Extracellular\s+9.97\s+Flagellar\s+PSORTb version" />
+				</assert_contents>
+            </output>
+		</test>
+	</tests>
+
+	<help>
+		<![CDATA[
+PSORTb predicts the subcellular localization of bacterial and archaeal proteins.
+
+Input requirements
+
+- Protein sequences in FASTA format. All sequences in one run should belong to the same organism class.
+
+Options
+
+- Organism type: select Gram-positive (`--positive`), Gram-negative (`--negative`), or Archaea (`--archaea`).
+- Output format: `normal` (human-readable), `terse` (tab-delimited), or `long` (tab-delimited with module details).
+- Cutoff (`-c`): threshold for final localization assignment (documentation suggests ~7.5).
+- Multiple localization cutoff (`-d`): threshold to flag possible multiple localization sites.
+- Exact (`--exact`): skip SCL-BLASTe step.
+
+Notes
+
+- PSORTb emphasizes precision; proteins with ambiguous signals may be reported as Unknown.
+- Long format includes module outputs and localization scores; terse/long are suitable for bulk processing.
+
+Reference
+
+https://psort.org/documentation/index.html
+		]]>
+	</help>
+
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq249</citation>
+	</citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psortb_arch.fa	Thu Dec 18 16:15:09 2025 +0000
@@ -0,0 +1,2 @@
+>YP_001689002.1
+MFEFITDEDERGQVGIGTLIVFIAMVLVAAIAAGVLINTAGYLQSKGSATGEEASAQVSNRINIVSAYGNVNNEKVDYVNLTVRQAAGADNINLTKSTIQWIGPDRATTLTYSSNSPSSLGENFTTESIKGSSADVLVDQSDRIKVIMYASGVSSNLGAGDEVQLTVTTQYGSKTTYWAQVPESLKDKNA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psortb_neg.fa	Thu Dec 18 16:15:09 2025 +0000
@@ -0,0 +1,2 @@
+>NP_949347.1
+MQGHHFGGDMSNSEAIDNTTAKLRLAQSSSLLALALLIGSAPAQAADTDWGWLAIGAPAATAQGWTGKGVVIGVVDTGIDFSHPALSGRAFDYNYGSFVAGSNHPHATHVAGIIGATDINRGMEGVAPDVRFSSMKIFTGAGGSYLGDAAVADAYDGAIGSGVRIFNNSWGSSDSIANFTSREELLAHEPLLVGAFTRAVNADAVLVWSTGNDGRSQPSWQAAAPYYIQELKANWIAVTSVGENGTIASYANACGVAKAWCLAAPGGDFNPGIYSTIPGKDYGYMSGTSMAAPYVTGATAIARQMFPKASGAQLAQIVLQTSRDIGAPGIDDVYGWGLLAVDNIVDTINPRGAALFASAAWGRFTTLSAIGNTVLDRISDLRNGRGDVVTAPLAFAG
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psortb_pos.fa	Thu Dec 18 16:15:09 2025 +0000
@@ -0,0 +1,2 @@
+>SAK_BPP42
+MLKRSLLFLTVLLLLFSFSSITNEVSASSSFDKGKYKKGDDASYFEPTGPYLMVNVTGVDGKRNELLSPRYVEFPIKPGTTLTKEKIEYYVEWALDATAYKEFRVVELDPSAKIEVTYYDKNKKKEETKSFPITEKGFVVPDLSEHIKNPGFNLITKVVIEKK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psortb_pos_output.txt	Thu Dec 18 16:15:09 2025 +0000
@@ -0,0 +1,22 @@
+SeqID: SAK_BPP42 
+  Analysis Report:
+    CMSVM+            Unknown                       [No details]
+    CWSVM+            Unknown                       [No details]
+    CytoSVM+          Unknown                       [No details]
+    ECSVM+            Extracellular                 [No details]
+    ModHMM+           Unknown                       [1 internal helix found]
+    Motif+            Unknown                       [No motifs found]
+    Profile+          Unknown                       [No matches to profiles found]
+    SCL-BLAST+        Extracellular                 [matched 134189: Staphylokinase precursor (Neutral proteinase) (Protease III)]
+    SCL-BLASTe+       Unknown                       [No matches against database]
+    Signal+           Non-Cytoplasmic               [Signal peptide detected]
+  Localization Scores:
+    Extracellular          9.98
+    Cellwall               0.02
+    CytoplasmicMembrane    0.00
+    Cytoplasmic            0.00
+  Final Prediction:
+    Extracellular          9.98
+
+-------------------------------------------------------------------------------
+