--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_run.xml	Sat Mar 02 07:43:50 2024 +0000
@@ -0,0 +1,98 @@
+<tool id="b2b_summarize_run" name="Summarize run" version="0.002">
+
+    <description>Summarize sequencing run and assembly statistics</description>
+
+    <!-- ***************************************************************** -->
+
+    <requirements>
+    <!--
+        <requirement type="package" version="0.003">b2b-utils</requirement>
+    -->
+        <requirement type="package" version="0.7.17">bwa</requirement>
+        <requirement type="package" version="0.008009">perl-biox-seq</requirement>
+        <requirement type="package" version="1.23">perl-file-which</requirement>
+    </requirements>
+
+    <!-- ***************************************************************** -->
+
+    <version_command>echo "0.002"</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+    perl $__tool_directory__/frag_lens
+        --forward "$in_filt1"
+        --reverse "$in_filt2"
+        --ref "$in_ref"
+        --threads  "\${GALAXY_SLOTS:-1}"
+        --max_aln 100000
+    | perl $__tool_directory__/summarize_run.pl
+        --raw_1     $in_raw1
+        --raw_2     $in_raw2
+        --filt_1    $in_filt1
+        --filt_2    $in_filt2
+        --consensus $in_ref
+        --bedgraph  $in_bg
+        --fastqc_1  $in_fqc1
+        --fastqc_2  $in_fqc2
+        --out       $report
+        --threads   "\${GALAXY_SLOTS:-1}"
+    ;
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+	    <param format="fastqsanger,fastq" name="in_raw1" type="data" label="Raw forward reads" />
+	    <param format="fastqsanger,fastq" name="in_raw2" type="data" label="Raw reverse reads" />
+	    <param format="fastqsanger,fastq" name="in_filt1" type="data" label="Filtered/synced forward reads" />
+	    <param format="fastqsanger,fastq" name="in_filt2" type="data" label="Filtered/synced reverse reads" />
+	    <param format="fasta" name="in_ref" type="data" label="Consensus (FASTA)" />
+	    <param format="bedgraph" name="in_bg" type="data" label="Coverage (bedgraph)" />
+	    <param format="txt" name="in_fqc1" type="data" label="Raw FastQC (forward reads)" />
+	    <param format="txt" name="in_fqc2" type="data" label="Raw FastQC (reverse reads)" />
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+       <data format="tabular" name="report" label="Run/assembly summary" />
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="in_raw1" value="sumrun_R1.fq" ftype="fastq" />
+            <param name="in_raw2" value="sumrun_R2.fq" ftype="fastq" />
+            <param name="in_filt1" value="sumrun_sync_R1.fq" ftype="fastq" />
+            <param name="in_filt2" value="sumrun_sync_R2.fq" ftype="fastq" />
+            <param name="in_ref" value="sumrun_ref.fa" ftype="fasta" />
+            <param name="in_bg" value="sumrun_ref.bg" ftype="bedgraph" />
+            <param name="in_fqc1" value="sumrun_R1.fastqc" ftype="txt" />
+            <param name="in_fqc2" value="sumrun_R2.fastqc" ftype="txt" />
+            <output name="report" file="sumrun.report.tsv" compare="diff" />
+        </test>
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+
+    `summarize_run` is a Galaxy-only utility from BASE2BIO that reports a
+    number of summary statistics for a sequencing run and assembly. It was
+    written to support workflows at the USDA Southeast Poultry Research
+    Laboratory and may be of limited general-purpose application.
+
+    </help>
+
+    <!-- ***************************************************************** -->
+
+    <citations>
+    </citations>
+
+</tool>
+