Mercurial > repos > wolma > mimodd_snpeff
changeset 1:99dfde12ee53 draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
| author | wolma |
|---|---|
| date | Mon, 18 Dec 2017 03:41:24 -0500 |
| parents | 01e09a4cacf7 |
| children | 9c5c2d4cf379 |
| files | annotate_variants.xml macros.xml |
| diffstat | 2 files changed, 37 insertions(+), 4 deletions(-) [+] |
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--- a/annotate_variants.xml Sat Nov 11 18:20:20 2017 -0500 +++ b/annotate_variants.xml Mon Dec 18 03:41:24 2017 -0500 @@ -31,7 +31,7 @@ #echo ' '.join(str($snpeff_settings.filter).split(',')) #end if --ofile '$ofile' - --verbose + --verbose --quiet ]]></command> <inputs> @@ -62,21 +62,26 @@ label="Name of an installed SnpEff genome" help="Your input needs to exactly match the name of an installed SnpEff database."> <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in SnpEff genome names." /> </param> </when> </conditional> <section name="codon_tables" title="Codon Table Configuration" expanded="false"> <param name="genome_codon_table" type="text" label="Genome codon table" - help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff." /> + help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff."> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." /> + </param> <repeat name="table_specs" default="0" min="0" title="Codon tables to use for specific contigs" help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above."> <param name="contig" type="text" label="contig or chromosome name"> <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator> + <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in contig/chromosome names" /> </param> <param name="table" type="text" label="uses codon table"> <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." /> </param> </repeat> </section>
--- a/macros.xml Sat Nov 11 18:20:20 2017 -0500 +++ b/macros.xml Mon Dec 18 03:41:24 2017 -0500 @@ -1,7 +1,7 @@ <macros> <token name="@MIMODD_VERSION_REQUIRED@">0.1.8</token> <token name="@MIMODD_REAL_VERSION@">0.1.8</token> - <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_0</token> + <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_1</token> <token name="@HELP_FOOTER@"><![CDATA[ ---- @@ -9,7 +9,7 @@ For **additional help** see these resources: -- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/v0.1.8/usage_toc.html>`__ +- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/doc0.1.8/usage_toc.html>`__ - The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:mimodd@googlegroups.com>`__ @@ -41,6 +41,34 @@ </citation> </citations> </xml> + <macro name="YYYY-MM-DD_format_validator"> + <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator> + </macro> + <macro name="known_sequencing_platform options"> + <option value="ILLUMINA">ILLUMINA</option> + <option value="PACBIO">PACBIO</option> + <option value="IONTORRENT">IONTORRENT</option> + <option value="ONT">ONT</option> + <option value="LS454">LS454</option> + <option value="SOLID">SOLID</option> + <option value="HELICOS">HELICOS</option> + <option value="CAPILLARY">CAPILLARY</option> + </macro> + <macro name="lex_sam_header" token_message="SAM header data may not contain non-ASCII characters."> + <validator type="expression" message="@MESSAGE@">not value or all(ord(c) < 127 for c in value)</validator> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove preset="string.whitespace" value="'" /> + <add value=" " /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + <add source="	" target=" " /> + <add source=" " target=" " /> + <add source=" " target=" " /> + </mapping> + </sanitizer> + </macro> </macros>