<tool id="ashlar" name="ASHLAR" version="@VERSION@.6" profile="17.09">
    <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description>
    <macros>
        <import>macros.xml</import>
    </macros>
 
    <expand macro="requirements"/>
    @VERSION_CMD@

    <command detect_errors="exit_code"><![CDATA[

        #def clean(file,type)
          #set name_clean = str($file.element_identifier).replace('.ome.tiff','').replace('.tiff','').replace('.tiff.','')

          #if $type == "raw"
            #set file_clean = $name_clean + ".ome.tiff"
          #elif $type == "ffp"
            #set file_clean = $name_clean + "_ffp.ome.tiff"
          #elif $type == "dfp"
            #set file_clean = $name_clean + "_dfp.ome.tiff"
          #end if

          #return $file_clean
        #end def

        ## Link the illumination files to appropriate file extension
        #for $dfp in $ldfp:
            ln -s "$dfp" "$clean($dfp,"dfp")" &&
        #end for
        #for $ffp in $lffp:
            ln -s "$ffp" "$clean($ffp,"ffp")" &&
        #end for

        @CMD_BEGIN@

        ## Supply the raw images
        #for $raw in $lraw:
            "$raw"
        #end for

        ## Additional arguments
        -m $max_shift

        #if $flip_x
        --flip-x
        #end if

        #if $flip_y
        --flip-y
        #end if

        -c $adv.align_channel

        #if $adv.filter_sigma
        --filter-sigma $adv.filter_sigma
        #end if

        #if $adv.tile_size
        --tile-size $adv.tile_size
        #end if

        --ffp
        #for $ffp in $lffp:
            "$clean($ffp,"ffp")"
        #end for
        --dfp
        #for $dfp in $ldfp:
            "$clean($dfp,"dfp")"
        #end for
        --pyramid
        -f registered.ome.tif;

        #if $upgrade.decide == "do_upgrade"
        python ${__tool_directory__}/pyramid_upgrade.py
        registered.ome.tif

        #if $upgrade.markers_file
        -n `python "$get_markers" "${upgrade.markers_file}"`
        #end if
        #end if
    ]]></command>

    <configfiles>
        <configfile name="get_markers">
import pandas as pd
import sys

marker_file = sys.argv[1]
df = pd.read_csv(marker_file)
print(' '.join(df['marker_name'].array)) 
        </configfile>
    </configfiles>



    <inputs>
        <param name="lraw" type="data_collection" format="tiff" collection_type="list" label="Raw Images"/>
        <param name="ldfp" type="data_collection" format="tiff" collection_type="list" label="Deep Field Profile Images"/>
        <param name="lffp" type="data_collection" format="tiff" collection_type="list" label="Flat Field Profile Images"/>

        <param name="flip_x" type="boolean" value="false" label="Flip X-axis"/>
        <param name="flip_y" type="boolean" value="false" label="Flip Y-axis"/>

        <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>

        <conditional name="upgrade">
            <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid">
                <option value="do_upgrade">Upgrade Pyramid</option>
                <option value="dont_upgrade">Leave Legacy Pyramid</option>
            </param>
            <when value="do_upgrade">
                <param name="markers_file" type="data" format="csv,tabular" optional="true" label="Markers File (optional)"/>
            </when>
            <when value="dont_upgrade">
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
            <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
            <param name="tile_size" type="integer"  optional="true" label="Cyto Mask Channel"/>
        </section>
    </inputs>

    <outputs>
        <data format="tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/>
    </outputs>
    <help><![CDATA[
Ashlar python package for microscopy registration, developed by HMS (repo: https://github.com/labsyspharm/ashlar)
        ashlar [-h] [-o DIR] [-c [CHANNEL]]
       [--output-channels [CHANNEL [CHANNEL ...]]] [-m SHIFT]
       [--filter-sigma SIGMA] [-f FORMAT] [--pyramid]
       [--tile-size PIXELS] [--ffp [FILE [FILE ...]]]
       [--dfp [FILE [FILE ...]]] [--plates] [-q] [--version]
       [FILE [FILE ...]]

Stitch and align one or more multi-series images

positional arguments:
  FILE                  an image file to be processed (one file per cycle)

optional arguments:
  -h, --help            show this help message and exit
  -o DIR, --output DIR  write output image files to DIR; default is the
                        current directory
  -c [CHANNEL], --align-channel [CHANNEL]
                        align images using channel number CHANNEL; numbering
                        starts at 0
  --output-channels [CHANNEL [CHANNEL ...]]
                        output only channels listed in CHANNELS; numbering
                        starts at 0
  -m SHIFT, --maximum-shift SHIFT
                        maximum allowed per-tile corrective shift in microns
  --filter-sigma SIGMA  width in pixels of Gaussian filter to apply to images
                        before alignment; default is 0 which disables
                        filtering
  -f FORMAT, --filename-format FORMAT
                        use FORMAT to generate output filenames, with {cycle}
                        and {channel} as required placeholders for the cycle
                        and channel numbers; default is
                        cycle_{cycle}_channel_{channel}.tif
  --pyramid             write output as a single pyramidal TIFF
  --tile-size PIXELS    set tile width and height to PIXELS (pyramid output
                        only); default is 1024
  --ffp [FILE [FILE ...]]
                        read flat field profile image from FILES; if specified
                        must be one common file for all cycles or one file for
                        each cycle
  --dfp [FILE [FILE ...]]
                        read dark field profile image from FILES; if specified
                        must be one common file for all cycles or one file for
                        each cycle
  --plates              enable plate mode for HTS data
  -q, --quiet           suppress progress display
  --version             print version

OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/ashlar
Conda Package Available From: https://anaconda.org/ohsu-comp-bio/ashlar
    ]]></help>
    <expand macro="citations" />
</tool>