comparison dada2_dada.xml @ 9:00f5005840fa draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1

8:2cfceb9f9b8e

## special case: for 1 sample the dada_result is not a list of dada
## objects but it is a dada object
#if $batch_cond.batch_select == "no":
    #if len($batch_cond.derep) > 1:
    for( id in names(dada_result) ){
        saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
    }
    #else
    #for $d in $batch_cond.derep:
        saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
    #end for
    #end if
#else
    saveRDS(dada_result, file='$dada')
#end if
    ]]></configfile>
    </configfiles>
    <inputs>

            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output_collection name="data_collection" type="list">
                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
                <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
            </output_collection>
        </test>
        <!-- default, batch -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="yes"/>
            <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
       </test>
        <!-- test non-default options -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="no"/>
            <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
            <param name="batch_cond|pool" value="pseudo"/>
            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output_collection name="data_collection" type="list">
                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Description
...........

9:00f5005840fa

## special case: for 1 sample the dada_result is not a list of dada
## objects but it is a dada object
#if $batch_cond.batch_select == "no":
    #if len($batch_cond.derep) > 1:
    for( id in names(dada_result) ){
        print(id)
        print(dada_result[[id]])
        saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
    }
    #else
    #for $d in $batch_cond.derep:
        print(dada_result)
        saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
    #end for
    #end if
#else
        print(dada_result)
    saveRDS(dada_result, file='$dada')
#end if
    ]]></configfile>
    </configfiles>
    <inputs>

            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output_collection name="data_collection" type="list">
                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
                <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
            </output_collection>
            <assert_stdout>
                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
            </assert_stdout>
        </test>
        <!-- default, batch -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="yes"/>
            <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
            <assert_stdout>
                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
            </assert_stdout>
       </test>
        <!-- test non-default options -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="no"/>
            <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
            <param name="batch_cond|pool" value="pseudo"/>
            <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
            <output_collection name="data_collection" type="list">
                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
            </output_collection>
            <assert_stdout>
                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
Description
...........