Mercurial > repos > peterjc > seq_length
comparison tools/seq_length/seq_length.xml @ 2:6f29bb9960ac draft
v0.0.3 - Fixed SFF; more tests
| author | peterjc |
|---|---|
| date | Mon, 14 May 2018 12:09:50 -0400 |
| parents | 458f987918a6 |
| children | fcdf11fb34de |
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| 1:458f987918a6 | 2:6f29bb9960ac |
|---|---|
| 1 <tool id="seq_length" name="Sequence lengths" version="0.0.2"> | 1 <tool id="seq_length" name="Sequence lengths" version="0.0.3"> |
| 2 <description>from FASTA, QUAL, FASTQ, or SFF file</description> | 2 <description>from FASTA, QUAL, FASTQ, or SFF file</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system --> | 4 <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system --> |
| 5 <requirement type="package" version="1.67">biopython</requirement> | 5 <requirement type="package" version="1.67">biopython</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <version_command> | 7 <version_command> |
| 8 python $__tool_directory__/seq_length.py --version | 8 python $__tool_directory__/seq_length.py --version |
| 9 </version_command> | 9 </version_command> |
| 10 <command detect_errors="aggressive"> | 10 <command detect_errors="aggressive"> |
| 11 python $__tool_directory__/seq_length.py '$input_file' '$input_file.ext' '$output_file' | 11 python $__tool_directory__/seq_length.py -i '$input_file' -f '$input_file.ext' -o '$output_file' |
| 12 </command> | 12 </command> |
| 13 <inputs> | 13 <inputs> |
| 14 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> | 14 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> |
| 15 </inputs> | 15 </inputs> |
| 16 <outputs> | 16 <outputs> |
| 18 </outputs> | 18 </outputs> |
| 19 <tests> | 19 <tests> |
| 20 <test> | 20 <test> |
| 21 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> | 21 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
| 22 <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" /> | 22 <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" /> |
| 23 <assert_stdout> | |
| 24 <has_line line="4 sequences, total length 3297" /> | |
| 25 </assert_stdout> | |
| 23 </test> | 26 </test> |
| 24 <test> | 27 <test> |
| 25 <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" /> | 28 <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" /> |
| 26 <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" /> | 29 <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" /> |
| 30 <assert_stdout> | |
| 31 <has_line line="2 sequences, total length 202" /> | |
| 32 </assert_stdout> | |
| 33 </test> | |
| 34 <test> | |
| 35 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> | |
| 36 <output name="output_file" file="MID4_GLZRM4E04_rnd30.length.tabular" ftype="tabular" /> | |
| 37 <assert_stdout> | |
| 38 <has_line line="30 sequences, total length 7504" /> | |
| 39 </assert_stdout> | |
| 27 </test> | 40 </test> |
| 28 </tests> | 41 </tests> |
| 29 <help> | 42 <help> |
| 30 **What it does** | 43 **What it does** |
| 31 | 44 |