Mercurial > repos > agpetit > concatenate_table

annotate concatenate_table.xml @ 5:da08087fcc0e draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
author agpetit
date Mon, 30 May 2022 14:12:50 +0000
parents 6364be33b0c2
children
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6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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1 <tool id="concatenate_table" name="concatenate lines of multi tables" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@">
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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2 <macros>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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3 <token name="@GALAXY_VERSION@">21.05</token>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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4 </macros>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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5 <requirements>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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6 </requirements>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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7 <command detect_errors="exit_code"><![CDATA[
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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8 #set $inter_file = "test.tabular"
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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9 #for $i, $input in enumerate($input_traj)
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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10 #if $i == 0
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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11 cat ${input} | awk -F'\t' 'BEGIN{mean="Time (ps)"; std=""} /^Time/ {for (i=2; i<(NF+1); i++) gsub(" ", ",mean ",\$i) ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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12 for (i=2; i<(NF+1); i++) mean=mean "\t" \$i ; for (i=2; i<(NF+1); i++) gsub(",mean", ",std ",\$i);
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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13 for (i=2; i<(NF+1); i++) std=std "\t" \$i } END{print (mean std)}' &>> '$sort_file' ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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14 #end if
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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15 #set $f=open(str($input), 'r')
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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16 #set $default_min = [x.rstrip().split()[0] for x in $f.readlines()][-1]
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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17 #set $default_min = float($default_min) * 10
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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18 cat ${input} | awk -F'\t' -v min=${default_min} 'BEGIN{min_val=min ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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19 max_val=0 ; means=""; std=""} /^[0-9]/ {if ($1 <= min_val) {min_val=$1} ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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20 if ($1 >= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i<NF; i++) means=means"\t"\$i ;means=means"\t"\$NF } ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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21 /Std/ {for (i=2; i<NF; i++) std=std"\t"\$i; ;std=std"\t"\$NF} END {print (min_val "-" max_val means std)}' &>> '$inter_file' ;
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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22 #end for
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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23 cat '$inter_file' | sort -k1 -n &>> '$sort_file'
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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24 ]]></command>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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25 <inputs>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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26 <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"/>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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27 </inputs>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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28 <outputs>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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29 <data name="sort_file" format="tabular" label="table_sort_pore_diameter_aqp.tabular"/>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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30 </outputs>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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31 <tests>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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32 <test>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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33 <param name="input_traj">
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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34 <collection type="list">
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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35 <element name="test_file1" value="PIP2.1_test_traj_1.tabular"/>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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36 <element name="test_file2" value="PIP2.1_test_traj_2.tabular"/>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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37 <element name="test_file3" value="PIP2.1_test_traj_3.tabular"/>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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38 </collection>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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39 </param>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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40 <output name="sort_file" file="table_sort_pore_diameter_aqp.tabular"/>
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41 </test>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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42 </tests>
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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43 <help><![CDATA[
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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44
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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45 .. class:: infomark
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46
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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47 **What it does**
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48
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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49 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.
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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50
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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51 _____
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52
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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53 .. class:: infomark
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54
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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55 **Inputs**
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56
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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57 - Collection of tables that contain the calculation of the pore diameter of an aquaporin for each subtrajectory
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58
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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59 _____
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60
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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61 .. class:: infomark
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62
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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63 **Outputs**
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64
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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65 - Table containing the average distance and standard deviation of each subpath for a complete trajectory
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66
6364be33b0c2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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67 ]]></help>
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68 <citations>
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69 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
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70 </citations>
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71 </tool>