--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_info.xml	Sun Sep 12 19:28:19 2021 +0000
@@ -0,0 +1,160 @@
+<tool id="fastq_info" name="FASTQ info" version="@TOOL_VERSION@+Galaxy@SUFFIX_VERSION@" profile="20.01">
+    <description>validates single or paired fastq files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        fastq_info
+        #if $input_option.input_type == 'single'
+            $input_option.fastq_1
+        #else
+            $input_option.fastq_1
+            $input_option.fastq_2
+        #end if
+        $r
+        $q
+        2>&1 | tee ./output.txt
+    ]]>    </command>
+    <inputs>
+        <conditional name="input_option">
+            <param name="input_type" type="select" label="Single reads or paired reads" help="Select between paired and single end data">
+                <option value="single">Single</option>
+                <option value="paired">Paired</option>
+            </param>
+            <when value="single">
+                <param name="fastq_1"  type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="Input FASTQ file"/>
+            </when>
+            <when value="paired">
+                <param name="fastq_1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: forward reads"/>
+                <param name="fastq_2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: reverse reads"/>
+            </when>
+        </conditional>
+        <param argument="-q" type="boolean" truevalue="" falsevalue="-q" checked="True" label="Determine quality scoring" help="If this option is disabled, it won't fail if the quality encoding cannot be determined" />
+        <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Skip check for duplicated readnames" help="By using this option no checks are made to determine if the read names/identifiers are unique (it will run faster and use less memory)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" from_work_dir="./output.txt" label="${tool.name} on ${on_string}: Validation result">
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="single"/>
+                <param name="fastq_1" value="R1.fastq"/>
+            </conditional>
+            <output name="output" file="output.txt" ftype="txt" lines_diff="2">
+                <assert_contents>
+                    <has_text text="OK"/>
+                    <has_size value="362" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!--Test gzip files-->
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="single"/>
+                <param name="fastq_1" value="R1.fastq.gz"/>
+            </conditional>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="OK"/>
+                    <has_size value="368" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!--Test paired reads-->
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="paired"/>
+                <param name="fastq_1" value="R1.fastq"/>
+                <param name="fastq_2" value="R2.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="OK"/>
+                    <has_size value="544" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test q option-->
+        <test expect_num_outputs="1">
+            <param name="q" value="False"/>
+            <conditional name="input_option">
+                <param name="input_type" value="single"/>
+                <param name="fastq_1" value="R1.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="OK"/>
+                    <has_size value="362" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test duplicated id -->
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="single"/>
+                <param name="fastq_1" value="R1_duplicated.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="line 36: duplicated sequence SRR1294492.1207358/1"/>
+                    <has_size value="311" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test r option-->
+        <test expect_num_outputs="1">
+            <param name="r" value="True"/>
+            <conditional name="input_option">
+                <param name="input_type" value="single"/>
+                <param name="fastq_1" value="R1_duplicated.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="OK"/>
+                    <has_size value="193" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test truncated file 01 -->
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="paired"/>
+                <param name="fastq_1" value="R1_truncated.fastq"/>
+                <param name="fastq_2" value="R2.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="line 32: file truncated"/>
+                    <has_size value="285" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test truncated file 02 -->
+        <test expect_num_outputs="1">
+            <conditional name="input_option">
+                <param name="input_type" value="paired"/>
+                <param name="fastq_1" value="R1_truncated_entry.fastq"/>
+                <param name="fastq_2" value="R2.fastq"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="unpaired read - SRR1294492.2047212/"/>
+                    <has_size value="557" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**Purpose**
+
+FASTQ info is part of `FASTQ utils <https://github.com/nunofonseca/fastq_utils>`_, a set of Linux utilities to validate and manipulate fastq files. 
+
+    ]]>    </help>
+    <expand macro="citations"/>
+</tool>