Mercurial > repos > wolma > mimodd_aln
changeset 1:e76e813f615a draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
| author | wolma |
|---|---|
| date | Mon, 18 Dec 2017 03:38:29 -0500 |
| parents | d801b0675eb5 |
| children | c254020c79db |
| files | macros.xml snap_caller.xml |
| diffstat | 2 files changed, 36 insertions(+), 4 deletions(-) [+] |
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--- a/macros.xml Sat Nov 11 18:18:54 2017 -0500 +++ b/macros.xml Mon Dec 18 03:38:29 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>
--- a/snap_caller.xml Sat Nov 11 18:18:54 2017 -0500 +++ b/snap_caller.xml Mon Dec 18 03:38:29 2017 -0500 @@ -165,7 +165,9 @@ help="Corresponds to the second value of the SNAP option -s."/> <param name="discard_overlapping_mates" type="text" optional="true" label="discard overlapping read pairs of type" - help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." /> + help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs."> + <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator> + </param> <param name="maxdist" type="integer" value="8" label="edit distance (default: 8)" help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/> @@ -329,7 +331,9 @@ help="Corresponds to the second value of the SNAP option -s."/> <param name="discard_overlapping_mates" type="text" optional="true" value="" label="discard overlapping read pairs of type" - help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs." /> + help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs."> + <validator type="expression" message="only RF, FR, FF, RR or ALL are allowed as input">not value or all(token.strip(' ') in ['RF', 'FR', 'FF', 'RR', 'ALL'] for token in value.split(','))</validator> + </param> <param name="maxdist" type="integer" optional="true" value="0" label="edit distance" help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/>