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comparison macros.xml @ 7:ff41a00a6745 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
author iuc
date Wed, 10 Aug 2022 13:17:22 +0000
parents fee85957cebe
children 34305b013402
comparison
equal deleted inserted replaced
6:fee85957cebe 7:ff41a00a6745
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.15.4</token> 2 <token name="@TOOL_VERSION@">3.15.4</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
7 <requirement type="package" version="3.0">zip</requirement> 7 <requirement type="package" version="3.0">zip</requirement>
8 <yield/> 8 <yield/>
41 <option value="--only-assembler">Only assembler (--only-assembler)</option> 41 <option value="--only-assembler">Only assembler (--only-assembler)</option>
42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option> 42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
43 </param> 43 </param>
44 </xml> 44 </xml>
45 45
46 <token name="@OMP_THREADS@"><![CDATA[
47 export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
48 ]]></token>
46 49
47 <!-- PREPARE INPUT FILES--> 50 <!-- PREPARE INPUT FILES-->
48 51
49 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[ 52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
50 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced" 53 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
736 </token> 739 </token>
737 <token name="@HELP_WID@"> 740 <token name="@HELP_WID@">
738 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. 741 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
739 </token> 742 </token>
740 <token name="@IONTORRENT@"><![CDATA[ 743 <token name="@IONTORRENT@"><![CDATA[
741 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. 744 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.
742 745
743 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. 746 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.
744 747
745 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. 748 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.
746 749