Mercurial > repos > iuc > raven
comparison raven.xml @ 1:f8564b2d7f63 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit cb3f04d604f2ce99f66b3d6e142d970063f9fd78"
| author | iuc |
|---|---|
| date | Mon, 13 Sep 2021 19:42:19 +0000 |
| parents | 33b7d8481a76 |
| children | 3edba9afc9bc |
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| 0:33b7d8481a76 | 1:f8564b2d7f63 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> | 2 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
| 3 <description>De novo assembly of Oxford Nanopore Technologies data</description> | 3 <description>De novo assembly of Oxford Nanopore Technologies data</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 | 7 |
| 53 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> | 53 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> |
| 54 </outputs> | 54 </outputs> |
| 55 <tests> | 55 <tests> |
| 56 <test expect_num_outputs="2"> | 56 <test expect_num_outputs="2"> |
| 57 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | 57 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> |
| 58 <output name="out_gfa" file="raven_gfa_assembly.txt"> | 58 <output name="out_gfa"> |
| 59 <assert_contents> | 59 <assert_contents> |
| 60 <has_n_lines n="2"/> | 60 <has_n_lines n="2"/> |
| 61 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> | |
| 61 </assert_contents> | 62 </assert_contents> |
| 62 </output> | 63 </output> |
| 63 <output name="out_fasta" file="raven_assembly.fasta"> | 64 <output name="out_fasta"> |
| 64 <assert_contents> | 65 <assert_contents> |
| 65 <has_n_lines n="2"/> | 66 <has_n_lines n="2"/> |
| 67 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> | |
| 66 </assert_contents> | 68 </assert_contents> |
| 67 </output> | 69 </output> |
| 68 </test> | 70 </test> |
| 69 <test expect_num_outputs="1"> | 71 <!-- <test expect_num_outputs="1"> |
| 70 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | 72 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> |
| 71 <param name="graphical_fragment_assembly" value="false"/> | 73 <param name="graphical_fragment_assembly" value="false"/> |
| 72 <output name="out_fasta" file="raven_assembly.fasta"> | 74 <output name="out_fasta"> |
| 73 <assert_contents> | 75 <assert_contents> |
| 74 <has_n_lines n="2"/> | 76 <has_n_lines n="2"/> |
| 77 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> | |
| 75 </assert_contents> | 78 </assert_contents> |
| 76 </output> | 79 </output> |
| 77 </test> | 80 </test> --> |
| 78 </tests> | 81 </tests> |
| 79 <help><![CDATA[ | 82 <help><![CDATA[ |
| 80 .. class:: infomark | 83 .. class:: infomark |
| 81 | 84 |
| 82 **What it does** | 85 **What it does** |