Mercurial > repos > peterjc > seq_primer_clip
comparison tools/primers/seq_primer_clip.xml @ 1:8c02a91a8680 draft
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
| author | peterjc |
|---|---|
| date | Tue, 30 Apr 2013 11:04:43 -0400 |
| parents | 945053d79e60 |
| children |
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| 0:945053d79e60 | 1:8c02a91a8680 |
|---|---|
| 1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8"> | 1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.9"> |
| 2 <description>Trim off 5' or 3' primers</description> | 2 <description>Trim off 5' or 3' primers</description> |
| 3 <version_command interpreter="python">seq_primer_clip.py --version</version_command> | 3 <version_command interpreter="python">seq_primer_clip.py --version</version_command> |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | 5 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file |
| 6 </command> | 6 </command> |
| 37 </change_format> | 37 </change_format> |
| 38 </data> | 38 </data> |
| 39 </outputs> | 39 </outputs> |
| 40 <tests> | 40 <tests> |
| 41 <test> | 41 <test> |
| 42 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> | 42 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> |
| 43 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 43 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 44 <param name="primer_type" value="Forward" /> | 44 <param name="primer_type" value="Forward" /> |
| 45 <param name="mm" value="2" /> | 45 <param name="mm" value="2" /> |
| 46 <param name="keep_negatives" value="false" /> | 46 <param name="keep_negatives" value="false" /> |
| 47 <param name="min_len" value="35" /> | 47 <param name="min_len" value="35" /> |
| 48 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> | 48 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> |
| 49 </test> | 49 </test> |
| 50 <test> | 50 <test> |
| 51 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> | 51 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> |
| 52 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 52 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 53 <param name="primer_type" value="Forward" /> | 53 <param name="primer_type" value="Forward" /> |
| 54 <param name="mm" value="2" /> | 54 <param name="mm" value="2" /> |
| 55 <param name="keep_negatives" value="false" /> | 55 <param name="keep_negatives" value="false" /> |
| 56 <param name="min_len" value="35" /> | 56 <param name="min_len" value="35" /> |
| 57 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> | 57 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> |
| 58 </test> | 58 </test> |
| 59 <test> | 59 <test> |
| 60 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> | 60 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> |
| 61 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 61 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 62 <param name="primer_type" value="Forward" /> | 62 <param name="primer_type" value="Forward" /> |
| 63 <param name="mm" value="2" /> | 63 <param name="mm" value="2" /> |
| 64 <param name="keep_negatives" value="false" /> | 64 <param name="keep_negatives" value="false" /> |
| 65 <param name="min_len" value="35" /> | 65 <param name="min_len" value="35" /> |
| 66 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> | 66 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> |
| 67 </test> | 67 </test> |
| 68 <test> | 68 <test> |
| 69 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> | 69 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> |
| 70 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 70 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 71 <param name="primer_type" value="Reverse" /> | 71 <param name="primer_type" value="Reverse" /> |
| 72 <param name="mm" value="2" /> | 72 <param name="mm" value="2" /> |
| 73 <param name="keep_negatives" value="true" /> | 73 <param name="keep_negatives" value="true" /> |
| 74 <param name="min_len" value="35" /> | 74 <param name="min_len" value="35" /> |
| 75 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> | 75 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> |
| 76 </test> | 76 </test> |
| 77 <test> | 77 <test> |
| 78 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> | 78 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> |
| 79 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 79 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 80 <param name="primer_type" value="Reverse" /> | 80 <param name="primer_type" value="Reverse" /> |
| 81 <param name="mm" value="2" /> | 81 <param name="mm" value="2" /> |
| 82 <param name="keep_negatives" value="true" /> | 82 <param name="keep_negatives" value="true" /> |
| 83 <param name="min_len" value="35" /> | 83 <param name="min_len" value="35" /> |
| 84 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> | 84 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> |
| 85 </test> | 85 </test> |
| 86 <test> | 86 <test> |
| 87 <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> | 87 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> |
| 88 <param name="primer_fasta" value="primers/dop_primers.fasta" /> | 88 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 89 <param name="primer_type" value="Reverse" /> | 89 <param name="primer_type" value="Reverse" /> |
| 90 <param name="mm" value="2" /> | 90 <param name="mm" value="2" /> |
| 91 <param name="keep_negatives" value="true" /> | 91 <param name="keep_negatives" value="true" /> |
| 92 <param name="min_len" value="35" /> | 92 <param name="min_len" value="35" /> |
| 93 <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | 93 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> |
| 94 </test> | 94 </test> |
| 95 </tests> | 95 </tests> |
| 96 <requirements> | 96 <requirements> |
| 97 <requirement type="python-module">Bio</requirement> | 97 <requirement type="python-module">Bio</requirement> |
| 98 </requirements> | 98 </requirements> |