Mercurial > repos > artbio > concatenate_multiple_datasets

annotate catWrapper.xml @ 2:1fe4d165ac0e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
author artbio
date Mon, 15 Apr 2019 18:52:43 -0400
parents 3a4694d4354f
children 62aebaf6cfa0
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2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
artbio
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1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.1.0">
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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2 <description>tail-to-head by specifying how</description>
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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3 <command><![CDATA[
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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4 #if $headers == 0:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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5 #set $concat_command = "cat"
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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6 #else:
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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7 #set $concat_command = 'tail -q -n +'+ str(int($headers)+1)
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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8 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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9 #if $global_condition.input_type == "singles":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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10 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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11 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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12 #for $file in $global_condition.inputs
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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13 '$file'
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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14 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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15 > '$out_file1'
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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16 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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17 #for $file in $global_condition.inputs
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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18 #if $file.ext[-2:] == "gz":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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19 printf "# ${file.element_identifier}\n" | gzip -c >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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20 gzip -dc "$file" | $concat_command |gzip -c >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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21 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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22 printf "# ${file.element_identifier}\n" >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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23 $concat_command "$file" >> '$out_file1' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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24 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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25 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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26 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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27 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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28 #else if $global_condition.input_type == "paired_collection":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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29 #if $global_condition.paired_cat_type == "by_strand":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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30 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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31 #for $file in $global_condition.inputs
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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32 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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33 $file['forward']
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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34 >> '$forward' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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35 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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36 $file['reverse']
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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37 >> '$reverse' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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38 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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39 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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40 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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41 #for $file in $global_condition.inputs.keys()
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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42 printf "# ${file}_forward\n" >> '$forward' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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43 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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44 $global_condition.inputs[$file]['forward']
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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45 >> '$forward' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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46 printf "# ${file}_reverse\n" >> '$reverse' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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47 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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48 $global_condition.inputs[$file]['reverse']
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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49 >> '$reverse' &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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50 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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51 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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52 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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53 #else if $global_condition.paired_cat_type == "by_pair":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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54 mkdir concatenated &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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55 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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56 #for $file in $global_condition.inputs.keys()
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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57 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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58 $global_condition.inputs[$file]['forward']
2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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59 > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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60 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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61 $global_condition.inputs[$file]['reverse']
2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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62 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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63 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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64 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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65 #else:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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66 #for $file in $global_condition.inputs.keys()
2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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67 printf "# ${file}_forward\n" > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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68 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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69 $global_condition.inputs[$file]['forward']
2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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70 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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71 printf "# ${file}_reverse\n" >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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72 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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73 $global_condition.inputs[$file]['reverse']
2
1fe4d165ac0e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 9f8e7a0dfea7761d71b9f2963f4686b4e892c2cf
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74 >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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75 #end for
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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76 sleep 1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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77 #end if
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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78 #else if $global_condition.paired_cat_type == "all":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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79 #if $dataset_names == "No":
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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80 #for $file in $global_condition.inputs.keys()
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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81 $concat_command
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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82 $global_condition.inputs[$file]['forward']
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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83 >> $out_file1 &&
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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84 $concat_command
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85 $global_condition.inputs[$file]['reverse']
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86 >> $out_file1 &&
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87 #end for
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88 sleep 1
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89 #else:
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90 #for $file in $global_condition.inputs.keys()
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91 printf "# ${file}_forward\n" > $out_file1 &&
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92 $concat_command
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93 $global_condition.inputs[$file]['forward']
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94 >> $out_file1 &&
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95 printf "# ${file}_reverse\n" >> $out_file1 &&
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96 $concat_command
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97 $global_condition.inputs[$file]['reverse']
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98 >> $out_file1 &&
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99 #end for
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100 sleep 1
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101 #end if
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102 #end if
0
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103 #end if
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104 ]]>
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105 </command>
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106 <inputs>
1
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107 <conditional name="global_condition">
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108 <param name="input_type" type="select" label="What type of data do you wish to concatenate?" help="Depending on the type of input selected the concatenation options will differ">
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109 <option value="singles">Single datasets</option>
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110 <option value="paired_collection">Paired collection</option>
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111 </param>
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112 <when value="singles">
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113 <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/>
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114 </when>
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115 <when value="paired_collection">
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116 <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collections to concatenate"/>
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117 <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
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118 <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
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119 <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
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120 <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option>
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121 </param>
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122 </when>
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123 </conditional>
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124 <param name="dataset_names" type="boolean" label="Include dataset names?" truevalue="Yes" falsevalue="No" checked="false" help="If 'Yes' is selected '#name of dataset' will be added when concatenating."/>
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125 <param name="headers" type="integer" label="Number of lines to skip at the beginning of each concatenation:" value="0" help="This paremeter exists so as to not concatenate comments or headers contained at the start of the files."/>
0
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126 </inputs>
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127 <outputs>
1
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128 <data name="out_file1" format_source="inputs" metadata_source="inputs" label="Concatenated datasets">
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129 <filter>global_condition['input_type'] == 'singles' or (global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all')</filter>
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130 </data>
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131 <collection name="paired_output" type="paired" label="Concatenation by strtand">
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132 <data name="forward" />
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133 <data name="reverse" />
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134 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
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135 </collection>
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136 <collection name="list_output" type="list" label="Concatenation by pairs">
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137 <discover_datasets pattern="(?P&lt;name&gt;.*)\.listed\.(?P&lt;ext&gt;.*)\.listed" visible="false" directory="concatenated"/>
1
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138 <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair'</filter>
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139 </collection>
0
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140 </outputs>
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141 <tests>
1
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142 <!-- Single files concatenation -->
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143 <test> <!-- Test 2 single files concatenation with no other option -->
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144 <param name="input_type" value="singles" />
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145 <param name="inputs" value="1.bed,2.bed"/>
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146 <param name="dataset_names" value="No" />
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147 <param name="headers" value="0" />
0
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148 <output name="out_file1" file="cat_wrapper_out1.bed"/>
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149 </test>
1
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150 <test> <!-- Test 2 single files concatenation with dataset names activated -->
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151 <param name="input_type" value="singles" />
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152 <param name="inputs" value="1.bed,2.bed"/>
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153 <param name="dataset_names" value="Yes" />
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154 <param name="headers" value="0" />
0
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155 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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156 </test>
1
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157 <test> <!-- Test 2 single files concatenation skipping 1 line -->
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158 <param name="input_type" value="singles" />
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159 <param name="inputs" value="1.bed,2.bed"/>
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160 <param name="dataset_names" value="No" />
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161 <param name="headers" value="1" />
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162 <output name="out_file1" file="cat_wrapper_out3.bed"/>
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163 </test>
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164 <test> <!-- Test gz handling with no options -->
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165 <param name="input_type" value="singles" />
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166 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
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167 <param name="dataset_names" value="No" />
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168 <param name="headers" value="0" />
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169 <output name="out_file1" file="1.fastq.gz" decompress="True"/>
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170 </test>
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171 <test> <!-- Test gz handling with options -->
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172 <param name="input_type" value="singles" />
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173 <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
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174 <param name="dataset_names" value="Yes" />
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175 <param name="headers" value="4" />
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176 <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
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177 </test>
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178 <!-- Test paired options -->
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179 <test> <!-- Test paired collection concatenation by_pair with no other option -->
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180 <param name="input_type" value="paired_collection" />
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181 <param name="paired_cat_type" value="by_pair"/>
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182 <param name="inputs">
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183 <collection type="list:paired">
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184 <element name="2">
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185 <collection type="paired">
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186 <element name="forward" value="2_f.fastq"/>
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187 <element name="reverse" value="2_r.fastq"/>
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188 </collection>
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189 </element>
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190 <element name="3">
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191 <collection type="paired">
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192 <element name="forward" value="3_f.fastq"/>
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193 <element name="reverse" value="3_r.fastq"/>
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194 </collection>
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195 </element>
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196 <element name="4">
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197 <collection type="paired">
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198 <element name="forward" value="4_f.fastq"/>
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199 <element name="reverse" value="4_r.fastq"/>
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200 </collection>
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201 </element>
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202 </collection>
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203 </param>
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204 <param name="dataset_names" value="No" />
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205 <param name="headers" value="0" />
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206 <output_collection name="list_output" type="list" >
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207 <element name="2" file="2.fastq"/>
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208 <element name="3" file="3.fastq"/>
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209 <element name="4" file="4.fastq"/>
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210 </output_collection>
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211 </test>
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212 <test> <!-- Test paired collection concatenation by_strand with no other option -->
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213 <param name="input_type" value="paired_collection" />
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214 <param name="paired_cat_type" value="by_strand"/>
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215 <param name="inputs">
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216 <collection type="list:paired">
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217 <element name="2">
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218 <collection type="paired">
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219 <element name="forward" value="2_f.fastq"/>
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220 <element name="reverse" value="2_r.fastq"/>
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221 </collection>
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222 </element>
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223 <element name="3">
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224 <collection type="paired">
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225 <element name="forward" value="3_f.fastq"/>
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226 <element name="reverse" value="3_r.fastq"/>
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227 </collection>
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228 </element>
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229 <element name="4">
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230 <collection type="paired">
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231 <element name="forward" value="4_f.fastq"/>
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232 <element name="reverse" value="4_r.fastq"/>
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233 </collection>
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234 </element>
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235 </collection>
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236 </param>
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237 <param name="dataset_names" value="No" />
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238 <param name="headers" value="0" />
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239 <output_collection name="paired_output" type="paired" >
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240 <element name="forward" file="f.fastq"/>
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241 <element name="reverse" file="r.fastq"/>
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242 </output_collection>
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243 </test>
0
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244 </tests>
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245 <help>
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246
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247 .. class:: warningmark
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248
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249 **WARNING:** This tool does not check if the datasets being concatenated are in the same format.
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250
1
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251 **WARNING:** The paired collection operations do not handle gziped files.
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252
0
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253 -----
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254
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255 **What it does**
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256
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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257 Concatenates datasets and paired collections with multiple options:
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258
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259 - It's possible select either a concatenation by strand, by pair or a whole collection concatenation, when the input is a paired collection.
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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260
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261 - Skipping lines before concatenation to avoid headers
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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262
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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263 - Add the name of the concatenated files as separator
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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264
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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265 -----
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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266
1
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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267 **Single datasets concatenation example**
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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268
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269 Concatenating Dataset::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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270
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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271 chrX 151087187 151087355 A 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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272 chrX 151572400 151572481 B 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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273
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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274 with Dataset1::
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275
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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276 chr1 151242630 151242955 X 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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277 chr1 151271715 151271999 Y 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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278 chr1 151278832 151279227 Z 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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279
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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280 and with Dataset2::
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281
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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282 chr2 100000030 200000955 P 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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283 chr2 100000015 200000999 Q 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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284
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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285 will result in the following::
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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286
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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287 chrX 151087187 151087355 A 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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288 chrX 151572400 151572481 B 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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289 chr1 151242630 151242955 X 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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290 chr1 151271715 151271999 Y 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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291 chr1 151278832 151279227 Z 0 -
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
artbio
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292 chr2 100000030 200000955 P 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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293 chr2 100000015 200000999 Q 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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294
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295 -----
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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296
1
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297 **Paired collection concatenation example**
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298
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299 1rst pair::
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300
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301 forward - reverse
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302
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303 2nd pair::
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304
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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305 forward - reverse
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306
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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307 Concatenation by strand::
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308
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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309 concatenates:
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310
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311 1rst forward + 2nd forward
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312 1rst reverse + 2nd reverse
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313
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314 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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315
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316 1 pair
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317
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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318 Concatenation by pair::
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319
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320 concatenates:
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321
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322 1rst forward + 1rst reverse
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323 2nd forward + 2nd reverse
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324
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325 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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326
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327 2 datasets
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328
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329 Concatenate all::
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330
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331 concatenates:
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332
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333 1rst forward + 1rst reverse + 2nd forward + 2nd reverse
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334
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335 outputs:
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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336
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337 1 dataset
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338
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339 -----
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340
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341 **When selecting "Include dataset names" when concatenating files**:
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342
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343 1rst file name="first_tabular"::
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344
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345 chrX 151087187 151087355 A 0 -
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346 chrX 151572400 151572481 B 0 +
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347
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artbio
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diff changeset
348 2nd file name="second_tabular"::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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349
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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350 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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351 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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352 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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353
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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354 output::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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355
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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356 # first_tabular
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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357 chrX 151087187 151087355 A 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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358 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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359 # second_tabular
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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360 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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361 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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362 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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363
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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364 -----
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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diff changeset
365
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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366 **Skiping lines**
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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367
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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368 1rst file::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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369
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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370 chrX 151087187 151087355 A 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
371 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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372
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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373 2nd file::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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374
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
375 chr1 151242630 151242955 X 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
376 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
377 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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378
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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diff changeset
379 skipping 1 line
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artbio
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380
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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381 output::
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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382
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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383 chrX 151572400 151572481 B 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
diff changeset
384 chr1 151271715 151271999 Y 0 +
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
parents: 0
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385 chr1 151278832 151279227 Z 0 -
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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386
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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387 -----
3a4694d4354f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
artbio
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388
0
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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389 Adapted from galaxy's catWrapper.xml to allow multiple input files.
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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390
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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391 </help>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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392 </tool>