--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_fx2tab.xml	Mon Oct 31 18:20:57 2022 +0000
@@ -0,0 +1,89 @@
+<tool id="seqkit_fx2tab" name="SeqKit fx2tab" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>convert FASTA/Q to tabular</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+
+#set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
+ln -s '${input}' '${input_identifier}' &&
+
+seqkit fx2tab 
+'${input_identifier}'
+$alphabet
+$avg_qual
+$gc
+$gc_skew
+$header_line
+$length
+$name
+$no_qual
+$only_id
+#if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
+    --qual-ascii-base 33
+#end if
+$seq_hash
+> '$output'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
+        <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/>
+        <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/>
+        <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/>
+        <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/>
+        <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/>
+        <param argument="--length" type="boolean" truevalue="--length" falsevalue="" checked="false" label="Output sequence length?"/>
+        <param argument="--name" type="boolean" truevalue="--name" falsevalue="" checked="false" label="Output only names (no sequences and qualities)?"/>
+        <param argument="--no_qual" type="boolean" truevalue="--no-qual" falsevalue="" checked="false" label="Eliminate qualities from output?"/>
+        <param argument="--only_id" type="boolean" truevalue="--only-id" falsevalue="" checked="false" label="Output id instead of full head?"/>
+        <param argument="--seq_hash" type="boolean" truevalue="--seq-hash" falsevalue="" checked="false" label="Output md5 hash of sequence?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <output name="output" file="fx2tab_output1.tabular" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="avg_qual" value="--avg-qual"/>
+            <param name="header_line" value="--header-line"/>
+            <param name="length" value="--length"/>
+            <param name="name" value="--name"/>
+            <param name="only_id" value="--only-id"/>
+            <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <output name="output" file="fx2tab_output3.tabular" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="alphabet" value="--alphabet"/>
+            <param name="avg_qual" value="--avg-qual"/>
+            <param name="gc" value="--gc"/>
+            <param name="gc_skew" value="--gc-skew"/>
+            <param name="header_line" value="--header-line"/>
+            <param name="length" value="--length"/>
+            <param name="name" value="--name"/>
+            <param name="no_qual" value="--no-qual"/>
+            <param name="only_id" value="--only-id"/>
+            <param name="seq_hash" value="--seq-hash"/>
+            <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Converts FASTA/Q to tabular format and adds columns for sequence length and GC content/GC skew.  The output
+consists of 3 columns; id, sequence and quality unless one of the options to output only names or to eliminate
+qualities is selected or additional columns (e.g., md5 sequence hash) are requested.
+    </help>
+    <expand macro="citations"/>
+</tool>
+