comparison stacks_gstacks.xml @ 1:27359c6bf3e3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"

0:d35cb34f2b85

    <expand macro="version_cmd"/>
    <command detect_errors="aggressive"><![CDATA[
@FASTQ_INPUT_FUNCTIONS@

mkdir bam_inputs stacks_outputs &&
#if $mode_cond.mode_select == "denovo" and not $popmap:
    ## since collections have no len .. yet
    #try:
        #set count = len($input_bam)
    #except:

    #else
        && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam
    #end if
#end if


## annoyingly gstacks creates stacks_output/gstacks.log
## instead of just writing to stderr as the other tools
## hence we do not use the tokens and return populations.log as log file and take the stderr
#if $output_log
    && mv stacks_outputs/gstacks.log $output_log
#end if

@EXTRACT_VCF@

## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
## alternative extra tool
## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)

                <param name="gt_alpha" value="0.1" />
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <has_text text="--ignore-pe-reads" />
                <has_text text="--rm-pcr-duplicates" />
                <has_text text="--kmer-length 23" />
                <has_text text="--max-debruijn-reads 666" />
                <has_text text="--min-kmer-cov 3" />
                <has_text text="--write-alignments" />
                <has_text text="--model marukihigh" />

            <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="refbased"/>
                <conditional name="paired_cond">
                    <param name="paired_select" value=""/>
                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
                    <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
                </conditional>
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <has_text text="-I bam_inputs" />
                <not_has_text text="-B " />
                <has_text text="--rm-unpaired-reads" />
                <has_text text="--rm-pcr-duplicates" />
            </assert_command>
        </test>
        <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
        <test expect_num_outputs="2">

                <conditional name="advanced_cond">
                    <param name="advanced_select" value="yes" />
                    <param name="min_mapq" value="23" />
                    <param name="max_clipped" value="0.23" />
                    <param name="max_insert_len" value="666" />
                    <param name="details" value="--detailed"/>
                    <param name="phasing_cooccurrences_thr_min" value="2"/>
                    <param name="phasing_cooccurrences_thr_max" value="3"/>
                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
                </conditional>
            </conditional>
            <param name="model_cond|model" value="snp"/>
            <param name="model_cond|gt_alpha" value="0.1" />
            <param name="model_cond|var_alpha" value="0.1" />
            <param name="add_log" value="yes" />
            <assert_command>
                <not_has_text text="-I bam_inputs" />
                <has_text text="-B " />
                <has_text text="--unpaired" />
                <has_text text="--min-mapq 23" />
                <has_text text="--max-clipped 0.23" />
                <has_text text="--max-insert-len 666" />
                <has_text text="--detailed" />
                <has_text text="--phasing-cooccurrences-thr-range 2,3" />
                <has_text text="--phasing-dont-prune-hets" />
                <has_text text="--model snp" />
                <has_text text="--gt-alpha 0.1" />
            </assert_command>

                    <param name="paired_select" value="--ignore-pe-reads"/>
                </conditional>
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <has_text text="-I bam_inputs" />
                <not_has_text text="-B " />
                <has_text text="--ignore-pe-reads" />
            </assert_command>
            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>

1:27359c6bf3e3

    <expand macro="version_cmd"/>
    <command detect_errors="aggressive"><![CDATA[
@FASTQ_INPUT_FUNCTIONS@

mkdir bam_inputs stacks_outputs &&

## annoyingly gstacks creates stacks_output/gstacks.log
## instead of just writing to stderr as the other tools
## hence we do not use the tokens and return populations.log as log file and take the stderr
#if $output_log
    ln -s '$output_log' stacks_outputs/gstacks.log &&
#end if

#if $mode_cond.mode_select == "denovo" and not $popmap:
    ## since collections have no len .. yet
    #try:
        #set count = len($input_bam)
    #except:

    #else
        && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam
    #end if
#end if

@EXTRACT_VCF@

## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
## alternative extra tool
## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)

                <param name="gt_alpha" value="0.1" />
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <has_text text="--ignore-pe-reads" />
                <has_text text="--kmer-length 23" />
                <has_text text="--max-debruijn-reads 666" />
                <has_text text="--min-kmer-cov 3" />
                <has_text text="--write-alignments" />
                <has_text text="--model marukihigh" />

            <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
            <conditional name="mode_cond">
                <param name="mode_select" value="refbased"/>
                <conditional name="paired_cond">
                    <param name="paired_select" value=""/>
                    <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails-->
                    <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
                </conditional>
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <not_has_text text="-I bam_inputs" />
                <has_text text="-B " />
                <not_has_text text="--rm-unpaired-reads" />
                <has_text text="--rm-pcr-duplicates" />
            </assert_command>
        </test>
        <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
        <test expect_num_outputs="2">

                <conditional name="advanced_cond">
                    <param name="advanced_select" value="yes" />
                    <param name="min_mapq" value="23" />
                    <param name="max_clipped" value="0.23" />
                    <param name="max_insert_len" value="666" />
                    <param name="details" value="--details"/>
                    <param name="phasing_cooccurrences_thr_min" value="2"/>
                    <param name="phasing_cooccurrences_thr_max" value="3"/>
                    <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
                </conditional>
            </conditional>
            <param name="model_cond|model" value="snp"/>
            <param name="model_cond|gt_alpha" value="0.1" />
            <param name="model_cond|var_alpha" value="0.1" />
            <param name="add_log" value="yes" />
            <assert_command>
                <has_text text="-I bam_inputs" />
                <not_has_text text="-B " />
                <has_text text="--unpaired" />
                <has_text text="--min-mapq 23" />
                <has_text text="--max-clipped 0.23" />
                <has_text text="--max-insert-len 666" />
                <has_text text="--details" />
                <has_text text="--phasing-cooccurrences-thr-range 2,3" />
                <has_text text="--phasing-dont-prune-hets" />
                <has_text text="--model snp" />
                <has_text text="--gt-alpha 0.1" />
            </assert_command>

                    <param name="paired_select" value="--ignore-pe-reads"/>
                </conditional>
            </conditional>
            <param name="add_log" value="yes" />
            <assert_command>
                <not_has_text text="-I bam_inputs" />
                <has_text text="-B " />
                <has_text text="--ignore-pe-reads" />
            </assert_command>
            <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
            <output_collection name="gstacks_out" type="list" count="2"/>
        </test>