--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopore_qc.xml	Sat Mar 02 03:35:34 2024 +0000
@@ -0,0 +1,132 @@
+<tool id="nanopore_qc" name="NanoporeQC" version="0.003">
+
+    <description>Quality report for nanopore data</description>
+
+    <requirements>
+        <requirement type="package" version="3.5.0">r-ggplot2</requirement>
+        <requirement type="package" version="1.1.4">r-dplyr</requirement>
+        <requirement type="package" version="1.3.1">r-tidyr</requirement>
+        <requirement type="package" version="2.1.5">r-readr</requirement>
+        <requirement type="package" version="2.3.8">r-yaml</requirement>
+        <requirement type="package" version="1.3.0">r-scales</requirement>
+        <requirement type="package" version="1.4.3">r-futile.logger</requirement>
+        <requirement type="package" version="1.14.10">r-data.table</requirement>
+        <requirement type="package" version="1.7.4">r-optparse</requirement>
+        <requirement type="package" version="0.88">perl-yaml-libyaml</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Unknown error" />
+        <exit_code range=":-1" level="fatal" description="Unknown error" />
+    </stdio>
+
+    <version_command>
+    <![CDATA[
+        echo '0.003'
+    ]]>
+    </version_command>
+
+    <command>
+    <![CDATA[
+
+        mkdir -p '${html_file.files_path}'
+
+        &&
+
+        Rscript '${__tool_directory__}/nanopore_qc.R'
+            -i '$input'
+            -o '${html_file.files_path}'
+            -q '$q_cutoff'
+            $discard_failed
+
+        &&
+
+        perl '${__tool_directory__}/yaml_to_html.pl'
+
+            '${html_file.files_path}/summary.yaml'
+            '${html_file.files_path}'
+            '$html_file'
+
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Basecall summary file from Albacore"/>
+        <param name="q_cutoff" type="float" value="10" min="0" label="Quality cutoff for QC calculations" />
+        <param name="discard_failed" type="boolean" checked="false" truevalue="--discard_failed T" falsevalue="" label="Ignore reads failing quality filter" />
+    </inputs>
+    <outputs>
+        <data format="html" name="html_file" label="NanoporeQC on ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- binary image blobs can differ, which is why we use line matching
+        instead of file matching -->
+
+        <!-- quality cutoff 10 -->
+        <test>
+            <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
+            <param name="q_cutoff" value="10" />
+            <output name="html_file">
+                <assert_contents>
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;7952&lt;/td&gt;" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- quality cutoff 6 -->
+        <test>
+            <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
+            <param name="q_cutoff" value="6" />
+            <output name="html_file">
+                <assert_contents>
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9254&lt;/td&gt;" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- quality cutoff 6, discard filtered -->
+        <test>
+            <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
+            <param name="q_cutoff" value="6" />
+            <param name="discard_failed" value="true" />
+            <output name="html_file">
+                <assert_contents>
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Dorado output -->
+        <test>
+            <param name="input" value="dorado.txt.small" ftype="tabular" />
+            <param name="q_cutoff" value="6" />
+            <output name="html_file">
+                <assert_contents>
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;31&lt;/td&gt;" />
+                    <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;29&lt;/td&gt;" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+    <help>
+<![CDATA[
+    `NanoporeQC` produces a QC report for nanopore sequencing data. It utilizes
+    the summary table produced by Albacore, which saves time by avoiding the
+    need to re-parse the FAST5 read data. `NanoporeQC` was originally forked
+    from the `minion_qc` codebase (https://github.com/roblanf/minion_qc).
+
+    There are only two tuneable parameters. The 'quality cutoff' sets a
+    threshold for plotting: two summaries are produced for each table and plot
+    -- one for all reads (with length >= 0) and one for reads with a quality
+    value greater than the cutoff. 'Ignore reads failing quality filter'
+    indicates whether to include or exclude failing reads from the QC plots.
+]]>
+    </help>
+    <citations>
+        <citation type='doi'>10.1093/bioinformatics/bty654</citation>
+    </citations>
+</tool>