comparison sam_dump.xml @ 7:c7620aa7e1f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1

6:30775c836c77

<tool id="sam_dump" name="Extract reads" version="@VERSION@">
    <description>in SAM or BAM format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>sam-dump --version</version_command>

        <![CDATA[
    #if $input.input_select=="file_list":
      for acc in `cat $input.file_list` ;
      do
    #elif $input.input_select=="accession_number":
      acc="$input.accession" &&
    #end if

    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
          [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
    #end if

        ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <param name="outputformat" type="select" label="select output format">
            <option value="bam">bam</option>
            <option value="sam">sam</option>
        </param>
        <section name="adv" title="Advanced Options" expanded="False">
            <param name="header" type="select" value="yes">

            </param>
            <expand macro="minMapq"></expand>
        </section>
    </inputs>
    <outputs>
        <collection name="output_collection" type='list'>
          <filter>input['input_select'] == "file_list"</filter>
          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
        </collection>
        <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
            <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}">
            <filter>input['input_select'] == "file"</filter>
            <change_format>
                <when input="outputformat" value="sam" format="sam"/>
            </change_format>
        </data>

            <param name="outputformat" value="sam"/>
            <param name="region" value="17:41243452-41277500"/>
            <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>
    <expand macro="citation"/>
</tool>

7:c7620aa7e1f0

<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>
    <expand macro="requirements"/>
    <version_command>sam-dump --version</version_command>

        <![CDATA[
    #if $input.input_select=="file_list":
      for acc in `cat $input.file_list` ;
      do
    #elif $input.input_select=="accession_number":
      acc="${input.accession}" &&
    #end if

    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
          [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
    #end if

        ]]>
    </command>
    <inputs>
        <expand macro="input_conditional"/>
        <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>
        <section name="adv" title="Advanced Options" expanded="False">
            <param name="header" type="select" value="yes">

            </param>
            <expand macro="minMapq"></expand>
        </section>
    </inputs>
    <outputs>
        <collection name="output_collection" type="list" label="SAM/BAM data (fastq-dump)">
          <filter>input['input_select'] == "file_list"</filter>
          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
        </collection>
        <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} (sam-dump)">
            <filter>input['input_select'] == "file"</filter>
            <change_format>
                <when input="outputformat" value="sam" format="sam"/>
            </change_format>
        </data>

            <param name="outputformat" value="sam"/>
            <param name="region" value="17:41243452-41277500"/>
            <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/>
        </test>
    </tests>
    <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>