diff seqkit_stats.xml @ 0:191738d53912 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_stats.xml	Wed Jun 01 05:38:38 2022 +0000
@@ -0,0 +1,59 @@
+<tool id="seqkit_stats" name="SeqKit statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>of FASTA/Q files</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}' '${input_identifier}' &&
+
+seqkit stats 
+'${input_identifier}'
+$all
+$basename
+#if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
+    --fq-encoding sanger
+#end if
+$skip_err
+$tabular
+> '$output'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
+        <param argument="--all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Output all statistics?" help="Includes quartiles of seq length, sum_gap, N50"/>
+        <param argument="--basename" type="boolean" truevalue="--basename" falsevalue="" checked="false" label="Output base name of input file?"/>
+        <param argument="--skip_err" type="boolean" truevalue="--skip-err" falsevalue="" checked="false" label="Skip errors?" help="Only show warning messages"/>
+        <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" label="Output machine-friendly tabular format?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt">
+            <change_format>
+                <when input="tabular" value="--tabular" format="tabular"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="all" value="--all"/>
+            <output name="output" file="stats_output1.tabular" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="all" value="--all"/>
+            <output name="output" file="stats_output2.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Outputs simple statistics of FASTA/Q files; number of sequences, sum / min / avg / max sequence lengths, Q1, Q2, Q3,
+sum gap, N50, Q20(%), and Q30(%).
+    </help>
+    <expand macro="citations"/>
+</tool>
+