Add seqkit sort to existing seqkit suite (#5909)

* add seqkit sort

* tiny changes

---------

Co-authored-by: Björn Grüning <[email protected]>

tools/seqkit/seqkit_sort.xml

@@ -0,0 +1,81 @@
+<tool id="seqkit_sort" name="SeqKit sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>FASTA or FASTQ files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #set $input_fn='input.' + str($input.ext)
+        #set $output_fn='seqkitsort_output.' + str($output.ext)
+
+        ln -s '$input' '$input_fn'
+        &&
+        seqkit sort
+        '$input_fn'
+        $reverse
+        $sort_by
+        -o '$output_fn'
+        --threads \${GALAXY_SLOTS:-4}
+
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
+        <param name="sort_by" type="select" label="Sort by:">
+            <option value="" selected="true">Sequence ID</option>
+            <option value="--by-bases">Non-gap bases</option>
+            <option value="--by-length">Sequence length</option>
+            <option value="--by-name">Full name (instead of just ID)</option>
+            <option value="--by-seq">Sequence</option>
+        </param>
+        <param argument="--reverse" type="boolean" truevalue="--reverse" falsevalue="" checked="false" label="Reverse the result?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" from_work_dir="seqkitsort_output.*" label="${input.name} sorted (${tool.name})"/>
+    </outputs>
+    <tests>
+        <!-- 1. fastq.gz -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <output name="output" file="sort_output1.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+        <!-- 2. fasta.gz -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <output name="output" file="sort_output2.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 3. by-bases, forward, fasta -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="sort_by" value="--by-bases"/>
+            <output name="output" file="sort_output3.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 4. by-length, rev, fasta -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="reverse" value="true"/>
+            <param name="sort_by" value="--by-length"/>
+            <output name="output" file="sort_output4.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 5. by-name, forward, fastq -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="sort_by" value="--by-name"/>
+            <output name="output" file="sort_output5.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+        <!-- 6. by-seq, rev, fastq -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="reverse" value="true"/>
+            <param name="sort_by" value="--by-seq"/>
+            <output name="output" file="sort_output6.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Sort sequences (FASTA, FASTQ) by id, name, sequence, or length.
+
+    </help>
+    <expand macro="citations"/>
+</tool>