Mercurial > repos > devteam > fasta_nucleotide_changer
comparison fasta_nucleotide_changer.xml @ 2:1cabf6626797 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:39:17 -0400 |
| parents | 8789a0450ad4 |
| children | ea1b0d77314d |
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| 1:8789a0450ad4 | 2:1cabf6626797 |
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| 1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > | 1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > |
| 2 <description>converter</description> | 2 <description>converter</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command> | 6 <command> |
| 7 <inputs> | 7 <![CDATA[ |
| 8 <param format="fasta" name="input" type="data" label="Library to convert" /> | 8 zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output' |
| 9 ]]> | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param format="fasta" name="input" type="data" label="Library to convert" /> | |
| 9 | 13 |
| 10 <param name="mode" type="select" label="Convert"> | 14 <param name="mode" type="select" label="Convert"> |
| 11 <option value="d">RNA to DNA (U to T)</option> | 15 <option value="d">RNA to DNA (U to T)</option> |
| 12 <option value="r">DNA to RNA (T to U)</option> | 16 <option value="r">DNA to RNA (T to U)</option> |
| 13 </param> | 17 </param> |
| 14 </inputs> | 18 </inputs> |
| 15 | 19 <outputs> |
| 16 <!-- | 20 <data format_source="input" name="output" metadata_source="input" /> |
| 17 Functional tests with param value starting with - fail. | 21 </outputs> |
| 18 --> | 22 <tests> |
| 19 <tests> | 23 <test> |
| 20 <test> | 24 <param name="input" value="fasta_nuc_changer1.fasta" /> |
| 21 <param name="input" value="fasta_nuc_changer1.fasta" /> | 25 <param name="mode" value="r" /> |
| 22 <param name="mode" value="r" /> | 26 <output name="output" ftype="fasta" file="fasta_nuc_change1.out" /> |
| 23 <output name="output" file="fasta_nuc_change1.out" /> | 27 </test> |
| 24 </test> | 28 <test> |
| 25 <test> | 29 <param name="input" value="fasta_nuc_changer2.fasta" /> |
| 26 <param name="input" value="fasta_nuc_changer2.fasta" /> | 30 <param name="mode" value="d" /> |
| 27 <param name="mode" value="d" /> | 31 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" /> |
| 28 <output name="output" file="fasta_nuc_change2.out" /> | 32 </test> |
| 29 </test> | 33 </tests> |
| 30 </tests> | 34 <help> |
| 31 | |
| 32 <outputs> | |
| 33 <data format="input" name="output" metadata_source="input" /> | |
| 34 </outputs> | |
| 35 | |
| 36 <help> | |
| 37 **What it does** | 35 **What it does** |
| 38 | 36 |
| 39 This tool converts RNA FASTA files to DNA (and vice-versa). | 37 This tool converts RNA FASTA files to DNA (and vice-versa). |
| 40 | 38 |
| 41 In **RNA-to-DNA** mode, U's are changed into T's. | 39 In **RNA-to-DNA** mode, U's are changed into T's. |
| 68 ------ | 66 ------ |
| 69 | 67 |
| 70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
| 71 | 69 |
| 72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
| 73 | 71 </help> |
| 74 </help> | |
| 75 </tool> | 72 </tool> |