Mercurial > repos > iuc > sra_tools
diff sam_dump.xml @ 7:c7620aa7e1f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
author | iuc |
---|---|
date | Wed, 10 May 2017 10:45:41 -0400 |
parents | 62e4d56ebb6f |
children | 6c60903f70ac |
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--- a/sam_dump.xml Wed Mar 22 05:23:31 2017 -0400 +++ b/sam_dump.xml Wed May 10 10:45:41 2017 -0400 @@ -1,5 +1,5 @@ -<tool id="sam_dump" name="Extract reads" version="@VERSION@"> - <description>in SAM or BAM format from NCBI SRA.</description> +<tool id="sam_dump" name="Extract reads in BAM" version="@VERSION@.2"> + <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> </macros> @@ -11,7 +11,7 @@ for acc in `cat $input.file_list` ; do #elif $input.input_select=="accession_number": - acc="$input.accession" && + acc="${input.accession}" && #end if #if $input.input_select=="file_list" or $input.input_select=="accession_number": @@ -91,7 +91,7 @@ </command> <inputs> <expand macro="input_conditional"/> - <param name="outputformat" type="select" label="select output format"> + <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> <option value="bam">bam</option> <option value="sam">sam</option> </param> @@ -113,18 +113,18 @@ </section> </inputs> <outputs> - <collection name="output_collection" type='list'> + <collection name="output_collection" type="list" label="SAM/BAM data (fastq-dump)"> <filter>input['input_select'] == "file_list"</filter> <discover_datasets pattern="(?P<designation>.+)\.bam" directory="." ext='bam'/> <discover_datasets pattern="(?P<designation>.+)\.sam" directory="." ext='sam'/> </collection> - <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> + <data name="output_accession" format="bam" label="${input.accession} (sam-dump)"> <filter>input['input_select'] == "accession_number"</filter> <change_format> <when input="outputformat" value="sam" format="sam"/> </change_format> </data> - <data name="output_file" format="bam" label="${input.file.name}.${outputformat}"> + <data name="output_file" format="bam" label="${input.file.name} (sam-dump)"> <filter>input['input_select'] == "file"</filter> <change_format> <when input="outputformat" value="sam" format="sam"/> @@ -140,11 +140,59 @@ <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> </test> </tests> - <help> - This tool extracts reads from sra archives using sam-dump. - The sam-dump program is developed at NCBI, and is available at - http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - @SRATOOLS_ATTRRIBUTION@ - </help> + <help><![CDATA[ +**What it does?** + +This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. + +**How to use it?** + +There are three ways in which you can download data: + + 1. Data for single accession + 2. Multiple datasets using a list of accessions + 3. Extract data from already uploaded SRA dataset + +Below we discuss each in detail. + +------ + +**Uploading data for a single accession** + +When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. As a result you will get a single BAM (or SAM) dataset in the history. + +----- + +**Uploading multiple datasets using a list of accessions** + +A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file: + + 1. Upload it into your history using Galaxy's upload tool + 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown + 3. Choose uploaded file within the **sra accession list** field + 4. Click **Execute** + +.. class:: warningmark + +BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. + +----- + +**Extract data from already uploaded SRA dataset** + +If a SRA dataset is present in the history, it can be converted into BAM dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number a single BAM dataset will be generated in the history. + +@ACCESSION_LIST_HOWTO@ + +----- + +.. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf +.. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html +.. _collection: https://galaxyproject.org/tutorials/collections/ +.. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies + + +@SRATOOLS_ATTRRIBUTION@ + ]]></help> <expand macro="citation"/> </tool>