--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pycoqc.xml	Tue Mar 02 21:09:07 2021 +0000
@@ -0,0 +1,97 @@
+<?xml version="1.0"?>
+<tool id="pycoqc" name="Pycoqc" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+
+    <expand macro="version_command"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+pycoQC
+--min_pass_qual '$min_pass_qual'
+--min_pass_len '$min_pass_len'
+#if $filter_calibration: 
+    '$filter_calibration'
+#end if
+#if $filter_duplicated:
+    '$filter_duplicated'
+#end if
+--min_barcode_percent '$min_barcode_percent'
+--report_title '$report_title'
+## TODO in future - --template_file
+## TODO in future - --config_file
+#if $skip_coverage_plot
+    '$skip_coverage_plot'
+#end if
+--sample '$sample'
+## TODO in future --default_config
+--summary_file '$summary_file'
+## TODO in future --barcode_file
+#if $bam_file:
+    --bam_file '$bam_file'
+#end if
+--html_outfile '$out_html'
+#if $out_json:
+    --json_outfile '$out_json'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--summary_file" type="data" format="txt,tabular" label="A sequencing_summary file" help="Must be generated by Albacore 1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+ (guppy_basecaller)"  />
+        <!-- <param argument="barcode_file" type="data" format="txt" label=""  /> -->
+        <param argument="--bam_file" type="data" format="bam" label="An alignment file generated by aligning the reads described in the sequencing_summary file" optional="true"/>
+        <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/>
+        <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'"  />
+        <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/>
+        <param argument="--filter_calibration" type="boolean" checked="false" truevalue="--filter_calibration" falsevalue="" label="Filter Calibration?" help="If yes, reads flagged as calibration strand by the basecaller are removed" />
+        <param argument="--filter_duplicated" type="boolean" checked="false" truevalue="--filter_duplicated" falsevalue="" label="Filter Duplicated?" help="If yes, duplicated read_ids are removed but the first occurence is kept (Guppy sometimes outputs the same read multiple times)" />
+        <param argument="--min_barcode_percent" type="float" value="0.1" label="Minimal percent of total reads to retain barcode label" help="If below, the barcode value is set as unclassified" />
+        <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" />
+        <param argument="--skip_coverage_plot" type="boolean" checked="false" truevalue="--skip_coverage_plot" falsevalue="" label="Skip the coverage plot in HTML report?" help="Useful when using a reference file containing many sequences, i.e. transcriptome" />
+        <param argument="--sample" type="integer" label="Number of reads will be randomly selected instead of the entire dataset for ploting function" help="(deterministic sampling)" value="100000"/>
+    </inputs>
+    <outputs>
+        <!-- standard -->
+        <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/>
+        <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary">
+            <filter>output_json_bool</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="2">
+            <param name="summary_file" value="test.txt"/>
+            <output name="out_html">
+                <assert_contents>
+                    <has_line line="&lt;!doctype html&gt;"/>
+                    <has_n_lines n="300"/>
+                </assert_contents>
+            </output>
+            <output name="out_json" file="test.json"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+**Input**
+
+- Guppy Sequencing Summary Output (tsv)
+- Aligned Reads (bam) (Optional)
+
+**Output**
+
+- Output QC Report (HTML)
+- Output QC Metrics (JSON)
+
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>