Mercurial > repos > nml > smalt
changeset 1:fae9ec82e10f draft
"planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
| author | nml |
|---|---|
| date | Wed, 17 Jun 2020 09:47:13 -0400 |
| parents | 51ad86498414 |
| children | 5ba47ab90254 |
| files | smalt_map.xml test-data/ecoli_1K_1.fq.gz test-data/ecoli_1K_2.fq.gz |
| diffstat | 3 files changed, 38 insertions(+), 9 deletions(-) [+] |
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--- a/smalt_map.xml Wed Sep 27 16:03:01 2017 -0400 +++ b/smalt_map.xml Wed Jun 17 09:47:13 2020 -0400 @@ -1,7 +1,11 @@ -<tool id="smalt" name="smalt" version="1.0.0" > +<tool id="smalt" name="smalt" version="@VERSION@+galaxy0"> <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description> + <macros> + <token name="@VERSION@">0.7.6</token> + <token name="@INPUT_TYPES@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> + </macros> <requirements> - <requirement type="package" version="0.7.6">smalt</requirement> + <requirement type="package" version="@VERSION@">smalt</requirement> <requirement type="package" version="1.5">samtools</requirement> </requirements> <stdio> @@ -132,11 +136,11 @@ <option value="collections">Paired-end Collections</option> </param> <when value="single"> - <param name="sInput1" type="data" format="fastq" label="Single end illumina fastq file" optional="false"/> + <param name="sInput1" type="data" format="@INPUT_TYPES@" label="Single end illumina fastq file" optional="false"/> </when> <when value="paired"> - <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> - <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/> + <param name="pInput1" type="data" format="@INPUT_TYPES@" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> + <param name="pInput2" type="data" format="@INPUT_TYPES@" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/> <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library"> <option value="pe">Illumina paired-end (short inserts)</option> <option value="mp">Illumina mate-pair library (long inserts)</option> @@ -144,7 +148,7 @@ </param> </when> <when value="collections"> - <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" /> + <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="@INPUT_TYPES@" collection_type="paired" /> <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library"> <option value="pe">Illumina paired-end (short inserts)</option> <option value="mp">Illumina mate-pair library (long inserts)</option> @@ -230,6 +234,20 @@ </assert_contents> </output> </test> + <test> + <param name="sPaired" value="paired"/> + <param name="pInput1" value="ecoli_1K_1.fq.gz"/> + <param name="pInput2" value="ecoli_1K_2.fq.gz"/> + <param name="pairtype" value="pe"/> + <param name="source" value="history"/> + <param name="reference" value="contigs.fasta"/> + <param name="outformat" value="sam"/> + <output name="output"> + <assert_contents> + <has_text text="SN:NODE_1_length_1000_cov_140.620106" /> + </assert_contents> + </output> + </test> </tests> <help> @@ -247,18 +265,18 @@ There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. - .. __: http://www.sanger.ac.uk/resources/software/smalt/ + .. __: https://www.sanger.ac.uk/tool/smalt-0/ ------ **Input formats** -SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger*). Use the FASTQ Groomer to prepare your files. +SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger* or *fastqsanger.gz*). Use the FASTQ Groomer to prepare your files. ------ -Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/". +Please cite the website "https://www.sanger.ac.uk/tool/smalt-0/". ------ @@ -367,4 +385,15 @@ <minid> specifies the number of exactly matching nucleotides either as a positive integer or as a fraction of the read length (<= 1.0). </help> + <citations> + <citation type="bibtex"> + @misc{smaltcitation, + author = {Ponstigl, Hannes}, + year = {2010}, + title = {smalt}, + publisher = {Wellcome Trust Sanger Institute, Cambridge, UK}, + journal = {Online}, + url = {https://www.sanger.ac.uk/tool/smalt-0/} + }</citation> + </citations> </tool>