comparison macros.xml @ 6:4a01e0d2892c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3

5:21da31ed41a1

<macros>
    <token name="@TOOL_VERSION@">3.15.4</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
            <requirement type="package" version="3.0">zip</requirement>
            <yield/>

            <option value="--only-assembler">Only assembler (--only-assembler)</option>
            <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
        </param>
    </xml>
    

<!-- PREPARE INPUT FILES-->

<token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
#if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"

    </token>
    <token name="@HELP_WID@">
SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
    </token>
    <token name="@IONTORRENT@"><![CDATA[
The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.

You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.

For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.

6:4a01e0d2892c

<macros>
    <token name="@TOOL_VERSION@">3.15.4</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
            <requirement type="package" version="3.0">zip</requirement>
            <yield/>

            <option value="--only-assembler">Only assembler (--only-assembler)</option>
            <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
        </param>
    </xml>
    
<token name="@OMP_THREADS@"><![CDATA[
export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
]]></token>

<!-- PREPARE INPUT FILES-->

<token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
#if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"

    </token>
    <token name="@HELP_WID@">
SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
    </token>
    <token name="@IONTORRENT@"><![CDATA[
The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://github.com/ablab/spades#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.

You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.

For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.