Mercurial > repos > peterjc > seq_length

diff tools/seq_length/seq_length.xml @ 2:6f29bb9960ac draft

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v0.0.3 - Fixed SFF; more tests
author peterjc
date Mon, 14 May 2018 12:09:50 -0400
parents 458f987918a6
children fcdf11fb34de
line wrap: on
line diff
--- a/tools/seq_length/seq_length.xml	Tue May 08 11:16:50 2018 -0400
+++ b/tools/seq_length/seq_length.xml	Mon May 14 12:09:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_length" name="Sequence lengths" version="0.0.2">
+<tool id="seq_length" name="Sequence lengths" version="0.0.3">
     <description>from FASTA, QUAL, FASTQ, or SFF file</description>
     <requirements>
         <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system -->
@@ -8,7 +8,7 @@
 python $__tool_directory__/seq_length.py --version
 </version_command>
     <command detect_errors="aggressive">
-python $__tool_directory__/seq_length.py '$input_file' '$input_file.ext' '$output_file'
+python $__tool_directory__/seq_length.py -i '$input_file' -f '$input_file.ext' -o '$output_file'
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
@@ -20,10 +20,23 @@
         <test>
             <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
             <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" />
+            <assert_stdout>
+                <has_line line="4 sequences, total length 3297" />
+            </assert_stdout>
         </test>
         <test>
             <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" />
             <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" />
+            <assert_stdout>
+                <has_line line="2 sequences, total length 202" />
+            </assert_stdout>
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30.length.tabular" ftype="tabular" />
+            <assert_stdout>
+                <has_line line="30 sequences, total length 7504" />
+            </assert_stdout>
         </test>
     </tests>
     <help>