--- a/fastq_name_affixer.xml	Thu Jul 27 09:46:13 2023 +0000
+++ b/fastq_name_affixer.xml	Wed Aug 02 11:31:12 2023 +0000
@@ -1,95 +1,110 @@
 <tool id="names_affixer" name="FASTQ Read name affixer" version="1.0.0">
-<description> Tool appending suffix and prefix to sequences names </description>
-<command interpreter="python">
-${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n $nspace > $output
-</command>
+    <description>Tool appending suffix and prefix to sequences names</description>
+    <required_files>
+        <include type="literal" path="name_affixer.py"/>
+    </required_files>
+    <command>
+        ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n
+        $nspace > $output
+    </command>
 
- <inputs>
-  <param format="fastq" type="data" name="input" label="Choose your FASTQ file" />
-  <param name="prefix" type="text" size="10" value="" label="Prefix" help="Enter prefix which will be added to all sequences names" />
-  <param name="suffix" type="text" size="10" value="" label="Suffix" help="Enter suffix which will be added to all sequences names"/>
-  <param name="nspace" type="integer" size="10" value="0" min="0" max="1000" label="Number of spaces in sequence name to ignore" help="Sequence name is a string before the first space. If you want name to include spaces in name, enter positive integer. All other characters beyond ignored spaces are omitted"/>
- </inputs>
+    <inputs>
+        <param format="fastq" type="data" name="input" label="Choose your FASTQ file"/>
+        <param name="prefix" type="text" size="10" value="" label="Prefix"
+               help="Enter prefix which will be added to all sequences names"/>
+        <param name="suffix" type="text" size="10" value="" label="Suffix"
+               help="Enter suffix which will be added to all sequences names"/>
+        <param name="nspace" type="integer" size="10" value="0" min="0" max="1000"
+               label="Number of spaces in sequence name to ignore"
+               help="Sequence name is a string before the first space. If you want name to include spaces in name, enter positive integer. All other characters beyond ignored spaces are omitted"/>
+    </inputs>
 
 
- <outputs>
- 	<data format="fastq" name="output" label="FASTQ dataset ${input.hid} with modified sequence names" />
- </outputs>
+    <outputs>
+        <data format="fastq" name="output"
+              label="FASTQ dataset ${input.hid} with modified sequence names"/>
+    </outputs>
+
+    <help>
+        **What is does**
 
- <help>
-**What is does**
- 
-Tool for appending prefix and suffix to sequences names in fastq formated sequences.
+        Tool for appending prefix and suffix to sequences names in fastq formated
+        sequences.
 
-**Example**
+        **Example**
+
+        The following Solexa-FASTQ file:
+
+        ::
 
-The following Solexa-FASTQ file:
- 
-::
- 
- @CSHL_4_FC042GAMMII_2_1_517_596
- GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
- +CSHL_4_FC042GAMMII_2_1_517_596
- 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
- 
-is renamed to:
+        @CSHL_4_FC042GAMMII_2_1_517_596
+        GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+        +CSHL_4_FC042GAMMII_2_1_517_596
+        40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
+        24 9 24 9 40 10 10 15 40
+
+        is renamed to:
+
+        ::
 
-::
- 
- @prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
- GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
- +prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
- 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+        @prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
+        GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+        +prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
+        40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
+        24 9 24 9 40 10 10 15 40
+
+        different format:
 
-different format:
- 
+
+        ::
 
-::
- 
- @HISEQ1:92:c0190acxx:8:1101:1252:2230 2:N:0:CGATGT
- AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
- +
- CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
-
-is renamed to:
+        @HISEQ1:92:c0190acxx:8:1101:1252:2230 2:N:0:CGATGT
+        AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
+        +
+        CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
 
-::
- 
- @prefixHISEQ1:92:c0190acxx:8:1101:1252:2230suffix
- AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
- +
- CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
- 
-note that string after first space is omitted! 
+        is renamed to:
+
+        ::
+
+        @prefixHISEQ1:92:c0190acxx:8:1101:1252:2230suffix
+        AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
+        +
+        CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
+
+        note that string after first space is omitted!
 
-Because sequence names sometimes containg spaces which delimit the actual name. By default, anything after spaces is 
-excluded from sequences name. In example sequence:
- 
-::
-  
- @SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
- CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
- +
- IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
+        Because sequence names sometimes containg spaces which delimit the actual name. By
+        default, anything after spaces is
+        excluded from sequences name. In example sequence:
+
+        ::
+
+        @SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
+        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
+        +
+        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
 
-when **Number of spaces in name to ignore** is set to 0 (default) the output will be:
- 
-::
- 
- @prefixSRR352150.23846180suffix
- CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
- +
- IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
- 
-If you want to keep spaces the setting **Number of spaces in name to ignore** to 1 will yield 
- 
-:: 
- 
- @prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
- CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
- +
- IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
- 
- 
-</help>
+        when **Number of spaces in name to ignore** is set to 0 (default) the output will
+        be:
+
+        ::
+
+        @prefixSRR352150.23846180suffix
+        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
+        +
+        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
+
+        If you want to keep spaces the setting **Number of spaces in name to ignore** to 1
+        will yield
+
+        ::
+
+        @prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
+        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
+        +
+        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
+
+
+    </help>
 </tool>