comparison bwa_macros.xml @ 26:2477830927ec draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33

25:e188dc7a68e6

<macros>
    <import>read_group_macros.xml</import>

    <token name="@VERSION@">0.7.17</token>

    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>

    <token name="@set_rg_string@">
        #set $rg_string = "@RG\\tID:" + str($rg_id)

    #end if
  ]]></token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">bwa</requirement>
            <requirement type="package" version="1.6">samtools</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />

                </when>
            </conditional>
        </actions>
    </macro>

    <token name="@RG@">
-----

.. class:: warningmark

 @RG     ID:FLOWCELL2.LANE3      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
 @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400

Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
    </token>
    <token name="@info@">
-----

.. class:: infomark

**More info**

To obtain more information about BWA and ask questions use these resources:

  1. https://biostar.usegalaxy.org/
  2. https://www.biostars.org/
  3. https://github.com/lh3/bwa
  4. http://bio-bwa.sourceforge.net/

    </token>
</macros>

26:2477830927ec

<macros>
    <import>read_group_macros.xml</import>

    <token name="@TOOL_VERSION@">0.7.18</token>

    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>

    <token name="@set_rg_string@">
        #set $rg_string = "@RG\\tID:" + str($rg_id)

    #end if
  ]]></token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bwa</requirement>
            <requirement type="package" version="1.20">samtools</requirement>
        </requirements>
    </xml>

    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">bwa</xref>
        </xrefs>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />

                </when>
            </conditional>
        </actions>
    </macro>

    <token name="@ref_genomes@">
**Indices: Selecting reference genomes for BWA**

The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
using the **Will you select a reference genome from your history or use a built-in index?** select box.

This select box has two options:

  1. **Use a built-in genome index**

     With this option (which is the default), Galaxy provides you with a dropdown select menu populated with genomes that have been pre-indexed with the bwa index utility and are ready to map sequenced reads against.

     The collection of pre-indexed genomes is managed by the administrators of your Galaxy instance. If your genome of interest is missing and its impractical to use the second option below to work with it, consider contacting the support team for the Galaxy server you are working on to let them know that you would like to have an additional genome indexed.

  2. **Use a genome from history and build index**

     With this option, Galaxy provides you with a dropdown select menu populated with all FASTA formatted files listed in your current history. If you have uploaded your genome of interest into your history it will be shown there.

     Selecting a genome from this dropdown will cause Galaxy to index it transparently first using the `bwa index` command, and then map against it with `bwa aln`.
    </token>
    <token name="@RG@">
-----

.. class:: warningmark

 @RG     ID:FLOWCELL2.LANE3      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
 @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400

Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
    </token>
    <token name="@links@">
.. _BWA: https://github.com/lh3/bwa
.. _`BWA manual`: https://bio-bwa.sourceforge.net/bwa.shtml
    </token>
</macros>