Adding rdeval #6778
Adding rdeval #6778
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tools/rdeval/rdeval.xml
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| #if $output_options.output_type.type_selector == "combined_reads" | ||
| ln -s '$reads_outfile' 'output.${output_type.format_selector}' && | ||
| #end if | ||
| rdeval --input-reads #echo " ".join([f"'{input}'" for $input in $mangled_inputs]) |
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Maybe a simple for loop is more readable and does not need the echo magic?
tools/rdeval/rdeval.xml
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| <param argument="--md5" type="boolean" checked="false" label="Print md5 of .rd files"/> | ||
| </when> | ||
| </conditional> | ||
| <param argument="--verbose" type="boolean" checked="false" label="Verbose output"/> |
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I would not offer this as a param for the user. Activate it by default, it does not hurt I guess.
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@richard-burhans do you need this param exposed to the user?
| </inputs> | ||
| <outputs> | ||
| <data name="stats_outfile" format="tabular" label="Rdeval summary"/> | ||
| <data name="rd_outfile" from_work_dir="output.rd" format="binary" label="RD File"> |
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What kind of format is that? Will it be used by downstream tools?
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
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To me it seems that we already have good tools for these tasks. What would be the advantage of having this tool?
Please do not get me wrong. Your implementation of the Galaxy tool is fine, but adding it to iuc comes with a long term commitment in maintenance. And I do not (yet see this justified).
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| <tool id="rdeval" name="rdeval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |||
| <description>Multithreaded read analysis and manipulation tool</description> | |||
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Description is quiet technical and at the same time non descriptive.
| </param> | ||
| <when value="no_file"/> | ||
| <when value="exclude_file"> | ||
| <param argument="--exclude-list" type="data" format="txt" optional="true" label="File containing headers to exclude"/> |
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Optional makes no sense in the conditional. Maybe skip the conditional and just have the two parameters as optional?
| <param argument="--include-list" type="data" format="txt" optional="true" label="File containing headers to include"/> | ||
| </when> | ||
| </conditional> | ||
| <param argument="--filter" type="text" optional="true" label="filter" help="e.g. l>1000 & q>20"/> |
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Unclear. Should we really offer it this way too users?
| <section name="input_subsample" title="Subsample input reads" expanded="false"> | ||
| <param argument="--sample" type="float" min="0" max="1" value="1" label="fraction of reads to subsample"/> | ||
| <param argument="--random-seed" type="integer" min="0" optional="true" label="random seed to make subsampling reproducible"/> | ||
| <param argument="--homopolymer-compress" type="integer" min="0" optional="true" label="Compress homopolymers longer than n in the input"/> |
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What does this mean?
| </param> | ||
| </when> | ||
| <when value="size"> | ||
| <param argument="--out-size" type="select" optional="true" label="size list type"> |
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Not sure what these options mean?
| </when> | ||
| </conditional> | ||
| <conditional name="output_type"> | ||
| <param name="type_selector" type="select" label="output type"> |
| <change_format> | ||
| <when input="format_selector" value="fasta.gz" format="fasta.gz"/> | ||
| <when input="format_selector" value="fastq.gz" format="fastq.gz"/> | ||
| <when input="format_selector" value="bam" format="bam"/> |
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This allows conversion from fasta to bam?
FOR CONTRIBUTOR: