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changeset 3:545d37b03fc7 draft

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The tag <organization name="SPAMR-VET Consortium"/> has been closed in the file fbqs_integrator.xm
author maciek
date Tue, 01 Jul 2025 09:03:17 +0000
parents ae0c6f433c1b
children ac6096e03113
files fbqs_integrator/fbqs_integrator.xml
diffstat 1 files changed, 72 insertions(+), 72 deletions(-) [+]
line wrap: on
line diff
--- a/fbqs_integrator/fbqs_integrator.xml	Tue Jun 24 10:36:47 2025 +0000
+++ b/fbqs_integrator/fbqs_integrator.xml	Tue Jul 01 09:03:17 2025 +0000
@@ -1,72 +1,72 @@
-<tool id="fbqs_integrator" name="FBQS Integrator" version="1.0.0" profile="21.05" license="GPL-3.0-or-later">
-    <description>Merge quality-checked outputs from Fastp, Bracken and QUAST into consolidated STARAMR Excel report</description>
-    
-    <requirements>
-        <requirement type="package" version="3.9">python</requirement>
-        <requirement type="package" version="1.5.3">pandas</requirement>
-        <requirement type="package" version="3.0.9">openpyxl</requirement>
-        <requirement type="package" version="1.21.0">numpy</requirement>
-    </requirements>
-
-    <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/fbqs-integrator.py'
-        --staramr '$staramr'
-        --fastp-jsons
-        #for $file in $fastp_jsons
-            '$file'
-        #end for
-        --quast-files
-        #for $file in $quast_files
-            '$file'
-        #end for
-        --output '$output'
-    ]]></command>
-
-    <inputs>
-        <param name="staramr" type="data" format="xlsx" label="Input STARAMR report (.xlsx)" 
-               help="STARAMR Excel report from upstream workflow"/>
-        <param name="fastp_jsons" type="data" format="json" multiple="true" 
-               label="Fastp/Bracken JSON outputs" 
-               help="JSON files from tooldistillator containing Fastp and Bracken results"/>
-        <param name="quast_files" type="data" format="json,tabular,csv" multiple="true" 
-               label="QUAST outputs" 
-               help="QUAST result files in JSON, TSV, or CSV format"/>
-    </inputs>
-
-    <outputs>
-        <data name="output" format="xlsx" label="Enhanced STARAMR report"/>
-    </outputs>
-
-    <help><![CDATA[
-**What it does**
-
-Integrates quality control outputs from the Abromics workflow into a unified STARAMR Excel report.
-
-**Quality Assessment**
-
-Automatically evaluates samples based on thresholds defined in your Python code:
-- Total reads after filtering: Warning <500k, Fail <400k
-- Read filtering ratio: Warning <0.8, Fail <0.6
-- Bracken main taxon proportion: Warning <90%, Fail <80%
-- Assembly metrics (N50, contigs, etc.)
-
-**Outputs**
-
-Enhanced Excel with additional sheets: FastP, Bracken, Quast, Quality_metrics
-    ]]></help>
-
-    <creator>
-        <organization name="SPAMR-VET Consortium">
-    </creator>
-
-    <citations>
-        <citation type="bibtex">
-@misc{fbqs_integrator,
-    author = {Diaconu, Elena Lavinia and Kochanowski, Maciej and Leclercq, Sebastien},
-    title = {FBQS Integrator},
-    year = {2025},
-    note = {SPAMR-VET Consortium (EUPAHW)}
-}
-        </citation>
-    </citations>
-</tool>
+<tool id="fbqs_integrator" name="FBQS Integrator" version="1.0.0" profile="21.05" license="GPL-3.0-or-later">
+    <description>Merge quality-checked outputs from Fastp, Bracken and QUAST into consolidated STARAMR Excel report</description>
+    
+    <requirements>
+        <requirement type="package" version="3.9">python</requirement>
+        <requirement type="package" version="1.5.3">pandas</requirement>
+        <requirement type="package" version="3.0.9">openpyxl</requirement>
+        <requirement type="package" version="1.21.0">numpy</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/fbqs-integrator.py'
+        --staramr '$staramr'
+        --fastp-jsons
+        #for $file in $fastp_jsons
+            '$file'
+        #end for
+        --quast-files
+        #for $file in $quast_files
+            '$file'
+        #end for
+        --output '$output'
+    ]]></command>
+
+    <inputs>
+        <param name="staramr" type="data" format="xlsx" label="Input STARAMR report (.xlsx)" 
+               help="STARAMR Excel report from upstream workflow"/>
+        <param name="fastp_jsons" type="data" format="json" multiple="true" 
+               label="Fastp/Bracken JSON outputs" 
+               help="JSON files from tooldistillator containing Fastp and Bracken results"/>
+        <param name="quast_files" type="data" format="json,tabular,csv" multiple="true" 
+               label="QUAST outputs" 
+               help="QUAST result files in JSON, TSV, or CSV format"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="xlsx" label="Enhanced STARAMR report"/>
+    </outputs>
+
+    <help><![CDATA[
+**What it does**
+
+Integrates quality control outputs from the Abromics workflow into a unified STARAMR Excel report.
+
+**Quality Assessment**
+
+Automatically evaluates samples based on thresholds defined in your Python code:
+- Total reads after filtering: Warning <500k, Fail <400k
+- Read filtering ratio: Warning <0.8, Fail <0.6
+- Bracken main taxon proportion: Warning <90%, Fail <80%
+- Assembly metrics (N50, contigs, etc.)
+
+**Outputs**
+
+Enhanced Excel with additional sheets: FastP, Bracken, Quast, Quality_metrics
+    ]]></help>
+
+    <creator>
+        <organization name="SPAMR-VET Consortium"/>
+    </creator>
+
+    <citations>
+        <citation type="bibtex">
+@misc{fbqs_integrator,
+    author = {Diaconu, Elena Lavinia and Kochanowski, Maciej and Leclercq, Sebastien},
+    title = {FBQS Integrator},
+    year = {2025},
+    note = {SPAMR-VET Consortium (EUPAHW)}
+}
+        </citation>
+    </citations>
+</tool>