comparison reheader.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

22:24154c580718

<tool id="reheader" name="Reheader BAM file" version="0.1.7.2">
  <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
  <expand macro="requirements"/>
  <version_command>python3 -m MiModD version -q</version_command>
  <command>    
    #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
      python3 -m MiModD header 
      #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form":

  
  <macros>
    <import>toolshed_macros.xml</import>
    <macro name="getreadgroupinfo">
        <conditional name="rginfo">
            <param name="source" type="select" label="source of new read-group information" help="">
                <option value="from_file">existing SAM file</option>
                <option value="from_form">input form</option>
            </param>
            <when value="from_file">
                <param name="data" type="data" format="sam" label="read-group template file in SAM format" help="use the read group information found in this file" />
              <repeat name="rg" title="custom read-group mapping" default="0" min="0" help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below.">
                <param name="source_id" type="text" label="modify input file information for read-group ID (will create the read-group if it does not exist)" />
                <param name="rg_id" type="text" label="with template file information for read-group ID" />
              </repeat>
            </when>
            <when value="from_form">
              <repeat name="rg" title="new read-group info" default="1" min="1">
                <param name="source_id" type="text" label="read-group ID (will create the read-group if it does not exist)" help="required field" />
                <param name="rg_id" type="hidden" value="" />
                <param name="rg_sm" type="text" label="sample name" help="required field" />
                <param name="rg_ds" type="text" label="description" />
                <param name="rg_date" type="text" label="date (YY-MM-DD format) the run was produced" />
                <param name="rg_cn" type="text" label="name of sequencing center" />
                <param name="rg_lb" type="text" label="read-group library" />
                <param name="rg_pl" type="text" label="platform/technology used to produce the reads" />
                <param name="rg_pi" type="text" label="predicted median insert size" />
                <param name="rg_pu" type="text" label="platform unit; unique identifier" />
              </repeat>    
            </when>
        </conditional>
    </macro>
  </macros>
  
  <inputs>

    <param name="inputfile" type="data" format="bam" label="input file in BAM format" help="the file to reheader." />

    <conditional name="rg">
        <param name="treat_rg" type="select" label="modify read-group information ?" help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone.">
            <option value="ignore">No, do not change read-groups.</option>
            <option value="update">Yes, update existing information</option>
            <option value="replace">Yes, replace existing information</option>
        </param>
        <when value="update">

            <expand macro="getreadgroupinfo" />
        </when>
    </conditional>
       
    <conditional name="co">
        <param name="treat_co" type="select" label="modify comments in the input file ?" help="">
            <option value="ignore">No, do not change comments.</option>
            <option value="update">Yes, append new comments to existing ones</option>
            <option value="replace">Yes, replace all existing comments</option>
        </param>
        <when value="update">
            <repeat name="coinfo" title="comment line" default="0" min="0">
                <param name="line" type="text" size="80" />
            </repeat>
        </when>
        <when value="replace">
            <repeat name="coinfo" title="comment line" default="0" min="0">
                <param name="line" type="text" size="80" />
            </repeat>
        </when>
    </conditional>

    <repeat name="rg_renaming" title="rename read-group" default="0" min="0" help="Warning: changing read-group IDs may increase job runtime substantially.">
        <param name="from" type="text" size="30" label="old name" help="as it appears in the current input file header"/>
        <param name="to" type="text" size="30" label="new name" />
    </repeat>
    
    <repeat name="sq_renaming" title="rename sequence" default="0" min="0" help="Warning: changing sequence names may increase job runtime substantially.">
        <param name="from" type="text" size="30" label="old name" help="as it appears in the current input file header"/>
        <param name="to" type="text" size="30" label="new name" />
    </repeat>
    
  </inputs>
  
  <outputs>
    <data name="output" format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}">
    </data>
  </outputs>

<help>
.. class:: infomark

 
The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool.

</help>
</tool>

23:5db0545b9004

<tool id="reheader" name="Reheader BAM file" version="0.1.7.3">
  <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
  <expand macro="requirements" />
  <version_command>python3 -m MiModD version -q</version_command>
  <command>    
    #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
      python3 -m MiModD header 
      #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form":

  
  <macros>
    <import>toolshed_macros.xml</import>
    <macro name="getreadgroupinfo">
        <conditional name="rginfo">
            <param help="" label="source of new read-group information" name="source" type="select">
                <option value="from_file">existing SAM file</option>
                <option value="from_form">input form</option>
            </param>
            <when value="from_file">
                <param format="sam" help="use the read group information found in this file" label="read-group template file in SAM format" name="data" type="data" />
              <repeat default="0" help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below." min="0" name="rg" title="custom read-group mapping">
                <param label="modify input file information for read-group ID (will create the read-group if it does not exist)" name="source_id" type="text" />
                <param label="with template file information for read-group ID" name="rg_id" type="text" />
              </repeat>
            </when>
            <when value="from_form">
              <repeat default="1" min="1" name="rg" title="new read-group info">
                <param help="required field" label="read-group ID (will create the read-group if it does not exist)" name="source_id" type="text" />
                <param name="rg_id" type="hidden" value="" />
                <param help="required field" label="sample name" name="rg_sm" type="text" />
                <param label="description" name="rg_ds" type="text" />
                <param label="date (YY-MM-DD format) the run was produced" name="rg_date" type="text" />
                <param label="name of sequencing center" name="rg_cn" type="text" />
                <param label="read-group library" name="rg_lb" type="text" />
                <param label="platform/technology used to produce the reads" name="rg_pl" type="text" />
                <param label="predicted median insert size" name="rg_pi" type="text" />
                <param label="platform unit; unique identifier" name="rg_pu" type="text" />
              </repeat>    
            </when>
        </conditional>
    </macro>
  </macros>
  
  <inputs>

    <param format="bam" help="the file to reheader." label="input file in BAM format" name="inputfile" type="data" />

    <conditional name="rg">
        <param help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone." label="modify read-group information ?" name="treat_rg" type="select">
            <option value="ignore">No, do not change read-groups.</option>
            <option value="update">Yes, update existing information</option>
            <option value="replace">Yes, replace existing information</option>
        </param>
        <when value="update">

            <expand macro="getreadgroupinfo" />
        </when>
    </conditional>
       
    <conditional name="co">
        <param help="" label="modify comments in the input file ?" name="treat_co" type="select">
            <option value="ignore">No, do not change comments.</option>
            <option value="update">Yes, append new comments to existing ones</option>
            <option value="replace">Yes, replace all existing comments</option>
        </param>
        <when value="update">
            <repeat default="0" min="0" name="coinfo" title="comment line">
                <param name="line" size="80" type="text" />
            </repeat>
        </when>
        <when value="replace">
            <repeat default="0" min="0" name="coinfo" title="comment line">
                <param name="line" size="80" type="text" />
            </repeat>
        </when>
    </conditional>

    <repeat default="0" help="Warning: changing read-group IDs may increase job runtime substantially." min="0" name="rg_renaming" title="rename read-group">
        <param help="as it appears in the current input file header" label="old name" name="from" size="30" type="text" />
        <param label="new name" name="to" size="30" type="text" />
    </repeat>
    
    <repeat default="0" help="Warning: changing sequence names may increase job runtime substantially." min="0" name="sq_renaming" title="rename sequence">
        <param help="as it appears in the current input file header" label="old name" name="from" size="30" type="text" />
        <param label="new name" name="to" size="30" type="text" />
    </repeat>
    
  </inputs>
  
  <outputs>
    <data format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}" name="output">
    </data>
  </outputs>

<help>
.. class:: infomark

 
The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool.

</help>
</tool>