Initial commit of Teloscope #6556
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In order to get the tests running here you need to add a |
…nto add-shed-yaml
Added .shed.yml, updated teloscope.xml, and added test-data
Added missing macros.xml
| </xml> | ||
| <token name="@TOOL_VERSION@">0.0.5</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">21.05</token> |
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I would prefer something in the range of 23.0 or 23.2
| <token name="@PROFILE@">21.05</token> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="bibtex"> |
| @@ -0,0 +1,108 @@ | |||
| <tool id="teloscope" name="Teloscope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |||
| <description>is a fast and comprehensive tool for matching, counting, and reporting telomeric repeats from genome assemblies.</description> | |||
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Please keep the description as short as possible: analyze telomeric repeats
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| mkdir -p output && |
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Indentation seems off
| <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose output"/> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="canonical_matches" format="bed" from_work_dir="output/canonical_matches.bed" label="Canonical matches from ${on_string}"> |
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There are quite a few outputs. Can some of them be optional? I would prefer labels of the form ${tool.name} on ${on_string}: ...
| ]]></command> | ||
| <inputs> | ||
| <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/> | ||
| <param argument="--canonical" type="text" value="TTAGGG" label="Canonical pattern"> |
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What is a canonical pattern?
| <valid initial="string.ascii_letters"/> | ||
| </sanitizer> | ||
| </param> | ||
| <param argument="--patterns" type="text" value="TTAGGG" label="Patterns to explore, separated by commas"> |
| <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/> | ||
| <param argument="--canonical" type="text" value="TTAGGG" label="Canonical pattern"> | ||
| <sanitizer invalid_char=""> | ||
| <valid initial="string.ascii_letters"/> |
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Can be more specific than ASCII letters, or?
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| teloscope [commands] |
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Would prefer not to have just command line help.
I get more and more reluctant to include completely undescribed software (at least I found no docs), I understand that this software comes from a respectful source. And probably users don't care anyway as long as the software does what they expect.
It's unsatisfying.
We should at the very least open an upstream issue that some docs would be nice.
FOR CONTRIBUTOR: