view concatenate_table.xml @ 13:2306bd893c55 draft default tip

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 83670d9ceed855c9f58e0fa63a682edcaace5354-dirty"

<tool id="concatenate_table" name="concatenate lines of multi tables" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@">
    <macros>
        <token name="@GALAXY_VERSION@">21.05</token>
    </macros>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $inter_file = "test.tabular"
        #for $i, $input in enumerate($input_traj)
            #if $i == 0
                cat ${input} | awk -F'\t' 'BEGIN{mean="Time (ps)"; std=""} /^Time/ {for (i=2; i<(NF+1); i++) gsub(" ", ",mean ",\$i) ;
                  for (i=2; i<(NF+1); i++) mean=mean "\t" \$i ;  for (i=2; i<(NF+1); i++) gsub(",mean", ",std ",\$i);
                  for (i=2; i<(NF+1); i++) std=std "\t" \$i } END{print (mean std)}'  &>> '$sort_file' ;
            #end if
            #set $f=open(str($input), 'r')
            #set $default_min = [x.rstrip().split()[0] for x in $f.readlines()][-1]
            #set $default_min = float($default_min) * 10
            cat ${input} | awk -F'\t' -v min=${default_min} 'BEGIN{min_val=min ;
                max_val=0 ; means=""; std=""} /^[0-9]/ {if ($1 <= min_val) {min_val=$1} ;
                if ($1 >= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i<NF; i++) means=means"\t"\$i ;means=means"\t"\$NF } ;
                /Std/ {for (i=2; i<NF; i++) std=std"\t"\$i; ;std=std"\t"\$NF} END {print (min_val "-" max_val means std)}' &>> '$inter_file' ;
        #end for
        cat '$inter_file' | sort -k1 -n &>> '$sort_file'
    ]]></command>
    <inputs>
        <param name="input_traj" type="data_collection" format="tabular" collection_type="list" label="Collection of tables containing the pore diameter of an aquaporin for a subtrajectory"/>
    </inputs>
    <outputs>
        <data name="sort_file" format="tabular" label="table_sort_pore_diameter_aqp.tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_traj">
                <collection type="list">
                    <element name="test_file1" value="PIP2.1_test_traj_1.tabular"/>
                    <element name="test_file2" value="PIP2.1_test_traj_2.tabular"/>
                    <element name="test_file3" value="PIP2.1_test_traj_3.tabular"/>
                </collection>
            </param>
            <output name="sort_file" file="table_sort_pore_diameter_aqp.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool allows to estimate the number of sub-trajectories to be created. It also allows to cut a path according to a desired number of sub-trajectories.

_____

.. class:: infomark

**Inputs**

    - Collection of tables that contain the calculation of the pore diameter of an aquaporin for each subtrajectory

_____

.. class:: infomark

**Outputs**

    - Table containing the average distance and standard deviation of each subpath for a complete trajectory

    ]]></help>
    <citations>
        <citation type="doi">10.1016/j.softx.2015.06.001</citation>
    </citations>
</tool>